Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Sirtuin (SIRT), in particular, by targeting natural antisense polynucleotides of a Sirtuin (SIRT). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Sirtuins (SIRT)s.

Abstract: Provided herein are methods of modulating the levels of total afucosylated (TAF) glycoforms of a recombinant glycosylated protein produced by glycosylation-competent cells in a cell culture. In exemplary embodiments, the methods comprise maintaining the cell culture at an initial set point pH for an initial cell culture period. Related compositions comprising glycosylated proteins and TAF glycoforms thereof are also provided herein.

Abstract: Provided herein are antisense agents for knocking down, inhibiting, or silencing expression of an HNF4?-P2 isoform mRNA in a cell or a patient. Also provided are methods of knocking down, inhibiting, or silencing expression of an HNF4?-P2 isoform mRNA in a cell or a patient and methods of treating a patient with liver disease, liver damage, liver inflammation, or liver failure, such as acute liver failure, ALD, AH, or ACLF.

Abstract: Control Devices are disclosed including RNA destabilizing elements (RDE), RNA control devices, and destabilizing elements (DE) combined with Chimeric Antigen Receptors (CARs) or other transgenes in eukaryotic cells. Multicistronic vectors are also disclosed for use in engineering host eukaryotic cells with the CARs and transgenes under the control of the control devices. These control devices can be used to optimize expression of CARs in the eukaryotic cells so that, for example, effector function is optimized. CARs and transgene payloads can also be engineered into eukaryotic cells so that the transgene payload is expressed and delivered after stimulation of the CAR on the eukaryotic cell.

Abstract: The present invention provides novel reagents and a cloning procedure based on homologous recombination for the site-directed cloning of a DNA fragment to a vector at designed site(s). The cloning reagents are made of mixture of extracts from at least two different cell types, preferably a mixture made of extracts from wild-type E. coli and S. Cerevisiae. Due to the activity of the mixture of cell extracts, recombination occurs between the 3? and 5?-ends of the target DNA and at the ends of linearized vector, which facilitates in-frame construction of expression vectors.

Abstract: The technology relates in part to biological methods for modifying carbon flux in cells, engineered cells and organisms in which cellular carbon flux has been modified, and methods of using engineered cells and organisms for production of organic molecules.

Abstract: This document provides materials and methods for generating oilseed (e.g., pennycress) plants that having low levels of erucic acid. For example, oilseed plants having reduced expression levels of one or more polypeptides involved in erucic acid metabolism (e.g., fatty acid elongase 1 (FAE1)), as well as materials and methods for making and using oilseed plants having low levels of erucic acid are provided.

Abstract: The invention relates to methods for increasing seed yield, increasing the total content of protein and/or lipid in seeds and reducing glucosinolate levels by reducing the expression or activity of UPL3. The invention also relates to genetically altered plants characterised by the above phenotypes and methods of producing such plants.

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

Abstract: The present invention is directed to a transgenic plant or a part thereof comprising a DNA capable of expressing an inhibitory nucleic acid molecule capable of inhibiting the expression of (a) KRE5 and/or KRE6 gene(s) in a fungus, to such DNA, to the inhibitory nucleic acid molecule, to a vector comprising the DNA, and to methods of producing the plant, of conferring fungal resistance to the plant, or of inhibiting the expression of the KRE5 and/or KRE6 gene(s) in a fungus, to the use of the DNA for inactivating a fungus, for protecting a plant against an infection by a fungus, or for inhibiting the expression of the KRE5 and/or KRE6 gene(s) in a fungus and to a composition comprising the DNA, vector or a dsRNA capable of inhibiting the expression of (a) KRE5 and/or KRE6 gene(s) in a fungus.

Abstract: The present invention relates to a cultivated melon (Cucumis melo spp. melo) plant resistant against Tomato Leaf Curl New Delhi virus (ToLCNDV), which comprises QTL-1 in its genome, and which QTL-1 confers resistance against Tomato Leaf Curl New Delhi virus (ToLCNDV). The invention further provides progeny, fruit, seeds, propagation material and food products from the plant. The invention also provides markers for the identification of QTL-1, as well as a method for testing a melon (Cucumis melo spp. melo) plant for the presence of QTL-1 in its genome and a method for selecting or identifying a melon plant resistant against ToLCNDV. Also provided is a method for producing a melon (Cucumis melo spp. melo) plant which is resistant against Tomato Leaf Curl New Delhi virus (ToLCNDV).

Abstract: The disclosure provides nucleic acids, and variants and fragments thereof, derived from strains of Bacillus thuringiensis encoding variant polypeptides having increased pesticidal activity against insect pests, including Lepidoptera and Coleopteran. Particular embodiments of the disclosure provide isolated nucleic acids encoding pesticidal proteins, pesticidal compositions, DNA constructs, and transformed microorganisms and plants comprising a nucleic acid of the embodiments. These compositions find use in methods for controlling pests, especially plant pests.

Abstract: Compositions and methods for controlling pests are provided. The methods involve transforming organisms with a nucleic acid sequence encoding an insecticidal protein. In particular, the nucleic acid sequences are useful for preparing plants and microorganisms that possess insecticidal activity. Thus, transformed bacteria, plants, plant cells, plant tissues and seeds are provided. Compositions are insecticidal nucleic acids and proteins of bacterial species. The sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest, as probes for the isolation of other homologous (or partially homologous) genes. The insecticidal proteins find use in controlling, inhibiting growth or killing lepidopteran, coleopteran, dipteran, fungal, hemipteran, and nematode pest populations and for producing compositions with insecticidal activity.

Abstract: The present invention encompasses compositions and methods to create a whole chromosome regulatable “kill” switch to inactivate expression of one or more therapeutic genes expressed from a synthetic chromosome.

Abstract: Disclosed is a viral vector comprising (a) a cDNA of a recombinant viral RNA having a sequence of a Borna disease viral genome comprising a disrupted G gene of the Borna disease viral genome and an inserted G gene of an avian bornaviral genome, wherein the cDNA of the recombinant viral RNA has at least an N gene, an X gene, a P gene and an L gene of the Borna disease viral genome in the same order as in the Borna disease viral genome and has an inserted foreign gene; (b) DNAs encoding ribozymes; and (c) a promoter sequence, wherein (b) the DNAs encoding ribozymes are located upstream and downstream of (a) the cDNA of the recombinant viral RNA, and (a) the cDNA of the recombinant viral RNA and (b) the DNAs encoding ribozymes are located downstream of (c) the promoter sequence.

Abstract: Compositions and methods are provided for treating ocular neuropathy in a subject. In one aspect, a recombinant adeno-associated viral vector is provided which includes a nucleic acid molecule comprising a sequence encoding NRF2. In another aspect, a recombinant adeno-associated viral vector is provided which includes a nucleic acid molecule comprising a sequence encoding SIRT1. In desired embodiments, the subject is human, cat, dog, sheep, or non-human primate.

Abstract: Methods of determining the stoichiometry of a viral capsid and/or determining the heterogeneity of protein components in a viral capsid are disclosed.

Abstract: Adeno-associated virus rh.20 sequences, vectors containing same, and methods of use are provided.

Abstract: The present invention relates nucleic acid constructs for the production of recombinant parvoviral (e.g. adeno-associated viral) vectors in insect cells, to insect cells comprising such constructs and to methods wherein the cells are used to produce recombinant parvoviral virions. The insect cells preferably comprise a first nucleotide sequence encoding the parvoviral rep proteins whereby the initiation codon for translation of the parvoviral Rep78 protein is a suboptimal initiation codon that effects partial exon skipping upon expression in insect cells. The insect cell further comprises a second nucleotide sequence comprising at least one parvoviral (AA V) inverted terminal repeat (ITR) nucleotide sequence and a third nucleotide sequence comprising a sequences coding for the parvoviral capsid proteins.

Abstract: Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.

Abstract: Provided herein are nucleic acids for expressing modified ligand-gated ion channel proteins in excitable cells or secretory cells, such as nerves and neurons and optionally including viral sequences, such as Adeno-associated virus sequences, for delivery to excitable cells or secretory cells of a patient. Also provided herein are methods of modulating cell membrane potentials in an excitable cell or secretory cell, and for treatment of a disease or disorder associated with the nervous system in a patient, such as chronic pain or itch.

Abstract: The invention provides processes for identifying and tracking genomic duplications that can occur during classical strain development or during the metabolic evolution of microbial strains originally constructed for the production of a biochemical through specific genetic manipulations, processes that stabilize the copy number of desirable genomic duplications using appropriate selectable markers, and non-naturally occurring microorganisms with stabilized copy numbers of a functional DNA sequence.

Abstract: The present invention relates to a system and method for efficiently modifying the genome of cells to treat diseases via sequential homologous recombination using CRISPR/Cas-mediated genome editing with donor DNA delivered by two or more adeno-associated virus (AAV) vectors.

Abstract: The present invention relates to methods for targeted insertion of at least one nucleic acid sequence/s of interest into a target genomic locus of a mammalian cell. More specifically, the methods of the invention are based on using nucleic acid cassettes comprising the nucleic acid sequence/s of interest and at least one recognition signal sequence (RSS), for insertion of the nucleic acid sequence of interest into the target genomic locus that is mediated by RAG-catalyzed recombination. The invention further provides cassettes, vectors and vehicles and cells comprising said cassettes, compositions and uses thereof in immunotherapy.

Abstract: Biological agent for bio-augmentation of an anaerobic digestion reactor, named first anaerobic digestion reactor, comprising a mixture of microorganisms including at least 10% of relative abundance in said mixture, of a unique Cloacimonetes sp. This agent is prepared by enrichment of a biological sample in a separate reactor fed with carbohydrate-rich substrate and oxygenated gas. Said agent comprising this unique Cloacimonetes sp. is able to restore and stabilize the biogas production of an anaerobic digestion reactor after acidosis, in a very short time.

Abstract: A method for the preparation of 2,4-dihydroxybutyric acid from homoserine includes a first step of conversion of the primary amino group of homoserine to a carbonyl group to obtain 2-oxo-4-hydroxybutyrate, and a second step of reduction of the obtained 2-oxo-4-hydroxybutyrate (OHB) to 2,4-dihydroxybutyrate.

Abstract: The aim of the invention is to provide a method for biotechnological production of carboxylic acids, in which the acid-forming micro-organisms are cultured in an unsterile manner in a submerged phase containing waste water containing all carbon and nutrient medium components necessary for the production of the carboxylic acid, which method avoids the disadvantages of known methods and enables high product concentrations and productivity while at the same time the resources of water and power are being conserved. This aim is achieved, according to the invention, in that micro-organisms are used that are cultured under unsterile conditions in a culture medium containing waste water with the addition of carbon-rich compounds.

Abstract: The present invention relates to variant thioesterases and their use in plants, e.g., to increase enzymatic activity and to promote increased production of mid-chain length fatty acids (e.g., 8 to 14 carbons) and at desired ratios. Further disclosed herein are methods of manufacturing renewable chemicals through the manufacture of novel triglyceride oils followed by chemical modification of the oils. Oils containing fatty acid chain lengths of C8, C10, C12 or C14 are also disclosed and are useful as feedstocks in the methods described herein.

Abstract: An aspartokinase variant, a microorganism comprising the variant, and a method for producing an aspartate-derived L-amino acid or a homoserine derivative thereof using the microorganism.

Abstract: According to the present invention, theanine can efficiently be produced without exogenously adding ethylamine and without accumulation or leftover of ethylamine as a byproduct, by using a microorganism having enhanced activity to produce ethylamine with acetaldehyde and alanine as substrates and having enhanced activity of ?-glutamylmethylamide synthetase or glutaminase.

Abstract: Disclosed herein are methods of producing hexoses from saccharides by enzymatic processes. The methods utilize fructose 6-phosphate and at least one enzymatic step to convert it to a hexose.

Abstract: The present invention relates to a system for production of ATP. This system is comprised of a support and one or more enzymes coupled to that support which are capable of collectively producing ATP from glucose or fructose metabolism. The present invention is additionally directed to a device, which includes the system, and to a method for carrying out a reaction involving the conversion of ATP to ADP using the system.

Abstract: The invention relates to a method for modifying a template double stranded polynucleotide, especially for characterization using nanopore sequencing. The method produces from the template a plurality of modified double stranded polynucleotides. These modified polynucleotides can then be characterized.

Abstract: The present disclosure provides, in some aspects, variant RNA polymerases, the use of which increases transcription efficiency while reducing the number of double-stranded RNA contaminates and run-on transcripts produced during an in vitro transcription reaction.

Abstract: The present invention discloses a production method of enzymatic reaction using adenosine instead of ATP. The method comprises the following steps: (1) adding ATP regeneration enzyme, AK enzyme and adenosine in proportion to carry out an enzymatic reaction in an enzymatic reaction system; (2) separating the ATP regeneration enzyme and AK enzyme by either directly separating ATP regeneration enzyme and AK enzyme immobilized in a reaction tank or separating free ATP regeneration enzyme and AK enzyme by an ultrafiltration membrane in a filter; and (3) separating and purifying the filtrate of step (2) to obtain a product. The disclosed method provides: greatly reduced industrial production costs; faster reaction rate; stable enzyme recovery system that is energy efficient and environmentally friendly; and capability of reusing the byproducts or collecting them for the production of ATP.

Abstract: Provided are a Streptomyces avermitilis strain C63-51 with a high yield of ivermectin B1b and a method for producing ivermectin B1b by using this strain. By using the above-mentioned strain and method, efficient production of single ivermectin B1b can be achieved.

Abstract: The present invention relates to recombinant protein production in algal cells. In particular, the present invention provides methods for making recombinant polypeptides in association with accumulated lipid particles or chloroplasts. The methods involve producing the recombinant polypeptide as a fusion polypeptide with an oil body protein and the growth of the algal cells under non-homeostatic conditions to form accumulated lipid particles within the algal cells, wherein the algal lipid particles contain the fusion polypeptide.

Abstract: The instant application provides a method for screening batches of soy hydrolysate for a desired amount of a component thereof, such as ornithine or putrescine, and selecting only those batches of soy hydrolysate that have a desired amount of such component. The present disclosure also sets forth methods for culturing cells in media supplemented with selected batches of soy to produce more consistent, high quality lots of a protein of interest. Further, the present disclosure provides a plurality of protein preparations that have each been produced by culturing cells in media supplemented with separate batches of soy hydrolysate containing a desired amount of ornithine or putrescine, whereby each batch of protein produced exhibits improved quality of the protein of interest or amount of quality protein produced.

Abstract: Disclosed herein are methods, compositions and kits for the synthesis of proteins which comprises unnatural amino acids that utilize a mutant tRNA.

Abstract: Disclosed are materials, devices, methods and systems for the detection of target molecules in test samples using microrobots. The target molecules may be bacterial toxins. The microrobots may include biohybrid materials such as porous spore core, a middle layer coated on the spore core for the actuation and steering in a fluid and further conjugation with a functional probe, and a sensing probe anchored onto middle layer for attaching to the targeted molecules in a fluid to respond to fluorescent tracking. A system for detecting bacterial toxin, is disclosed and comprises an intelligent motion control system based on automated fluorescent recognition and detection methods, which can propel and guide the microrobots to realize the automated motion in a pre-designed path and perform the real-time monitoring when integrating with an inverted fluorescent microscope or a fluorescent emission multi-reader.

Abstract: Phenotyping of cells involves loading a biological sample into a microfluidic device (1, 100) comprising cell compartments (20, 120) to capture biological material, including target cells, in the sample in the cell compartments (20, 120). A subset (20A) of the cell compartments (20, 120) is identified as comprising target cells exhibiting target phenotype characteristic(s) as determined based on monitoring biological material in the cell compartments (20, 120) prior to addition of a test agent. The biological material is exposed to a test agent and a phenotypic response of the target cells to the test agent is determined based on monitoring target cells in the identified subset (20A) of the cell compartments (20, 120). The phenotyping of the target cells is thereby not overshadowed by the response of other cells and non-cell material present in the biological sample.

Abstract: Antimicrobial resistance (AMR), the ability of a bacterial species to resist the action of an antimicrobial drug, has been on the rise due to the widespread use of antimicrobial agents, and one of the many ways AMR can spread is through contaminated water sources. To monitor these water sources, we have developed an inexpensive, fast assay using a paper-based analytical device (PAD) that can test for the presence of ?-lactamase-mediated resistance as one major form of AMR that has reliably detected resistance in sewage water.

Abstract: Apparatus and methods for measuring a concentration of a target molecule from a biological sample are disclosed. For example, the apparatus comprises a porous pad, which is impregnated with a solution containing at least one agent and contains an unfilled capillary matrix, a housing for the porous pad, and a membrane that covers the porous pad.

Abstract: The invention provides an enzymatic method for measuring the concentration of one or more analytes in the plasma portion of a blood derived sample, containing a first and a second component, where said second component interferes with the measurement of said first component.

Abstract: The present technology relates generally to methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications. In some embodiments, highly accurate, error corrected and massively parallel sequencing of nucleic acid material is possible using a combination of uniquely labeled strands in a double-stranded nucleic acid complex in such a way that each strand can be informatically related to its complementary strand, but also distinguished from it following sequencing of each strand or an amplified product derived therefrom. In various embodiments, this information can be used for the purpose of error correction of the determined sequence.

Abstract: The present invention provides a method for integrally detecting nondestructive measurement information and genome-related information of single cells. More specifically, the present invention uses a method including: preparing a plurality of compartments containing single cell or a derivative thereof, a first bead(s), and a second bead(s) per compartment; detecting both nondestructive measurement information of single cell and imaging information of the first bead(s) and associating the nondestructive measurement information of single cell with the imaging information of the first bead(s) before preparation of each compartment or in each compartment; obtaining a hybridized complex; producing an amplified product derived from the hybridized complex; and integrally detecting nondestructive measurement information and genome-related information in single cell.

Abstract: Provided are methods, as well as compositions, kits, and systems for preparing optimized control nucleic acids (polynucleotides) having reduce nucleic acid damage. Provided nucleic acid compositions provide reduced artifacts as compared to nucleic acid compositions prepared by conventional methods. Provided compositions are useful control in a variety of applications, including, but not limited to sequencing workflows to effectively monitor sensitivity, accuracy and/or precision of data.

Abstract: The present disclosure provides methods for the amplification and sequencing of the immune repertoire using barcoded oligonucleotides with molecular identifiers (MIDs). Further provided are methods for clustering-based data analysis of the sequencing reads to determine the immune repertoire.

Abstract: Automated methods for detecting cancer and related hyperplasias in biological samples.

Abstract: In an aspect, a method for evaluating the partitioning of nucleic acid molecules in a sample of polynucleotides based on epigenetic state, comprising: (a) adding a set of epigenetic-control nucleic acid molecules to the nucleic acid molecules in the sample of polynucleotides, whereby producing a spiked-in sample; (b) partitioning nucleic acid molecules of the spiked-in sample into plurality of partitioned sets; (c) enriching a subset of molecules from the plurality of partitioned sets to generate enriched molecules, wherein the enriched molecules comprises a group of epigenetic-control nucleic acid molecules and a group of nucleic acid molecules from the sample of polynucleotides; (d) sequencing the enriched molecules to produce sequencing reads; (e) analyzing the sequencing reads to generate one or more epigenetic partition scores of the epigenetic-control nucleic acid molecules; and (f) comparing the one or more epigenetic partition scores with one or more epigenetic partition cut-offs.