Abstract: Provided is a method for high-efficiently reading through a nonsense mutation site in a pathogenic gene in a monogenic hereditary disease and restoring the normal structure and function of a mutant protein, by using a genetic code expanded non-natural amino acid system. By modifying a tRNA of Methanosarcina barkeri (tRNAPyl), an all-new UAA and UGA encoded non-natural amino acid system that has high read-through efficiency is obtained, and the range of using the orthogonal pair of tRNAPyl and pyrrolysyl-tRNA synthetase (PylRS) is expanded. A plasmid mimicking the endogenous premature termination codon is constructed, so as to evaluate the efficiency of reading through the endogenous premature termination codon. Also provided is a system mainly comprising pathogenic genes of monogenic hereditary diseases and tumor inhibitory genes in tumor cells.

Abstract: The present invention relates to a chirally-modified dsRNA agent capable of inhibiting the expression of a target gene. The sense and antisense strands of chirally-modified dsRNA agent independently or in combination comprises one or more site specific-site specific/position specific, chirally-modified internucleotide linkages.

Abstract: The present disclosure provides for methods and compositions for treating cancer. A subject having lymphoma is administered an EZH2 inhibitor and an HDAC inhibitor. The combination of the EZH2 inhibitor and the HDAC inhibitor produces a synergistic effect on the cancer compared to the effect of the EZH2 inhibitor or the HDAC inhibitor alone.

Abstract: The present disclosure provides, in part, methods of discovering immunotherapy targets in vivo, therapeutic compositions (e.g., shRNA, immunoresponsive cells expressing shRNA and/or a chimeric antigen receptors (CAR)), and methods of use thereof.

Abstract: Embodiments of the disclosure include compositions and methods for generating RNA nanostructures, particularly in a cell. In particular embodiments, RNA subunits comprising at least one three-way junction and at least one kissing loop are configured such that multiple RNA subunits can polymerize into a specific structure. In particular embodiments, the RNA subunits are configured such that sequence of at least one kissing loop is complementary to sequence of another kissing loop, such as on another RNA subunit, and the summation of multiple RNA subunits having specific individual structures results in a combined polymerized structure of a defined shape. In specific embodiments, an RNA nanostructure generated from methods herein is utilized for an application, such as manufacturing or genetic modifications in a cell.

Abstract: The present invention relates to a nucleic acid coding for a human DGKk protein lacking a functional Proline Rich Region and/or a functional EPAPE repeated Region, and to its use in the treatment of fragile X syndrome in a patient in need thereof.

Abstract: System for producing a nucleic acid construct of interest, said system comprising: a set of n entry DNAs numbered 1 to n, n being an integer of at least 2, each of said n entry DNAs comprising in this order: (i) a type IIs restriction endonuclease recognition site followed by the cleavage site thereof; (ii) a sequence portion linking the cleavage site of said recognition site of item (i) with the cleavage site of the recognition site of the following item (iii), and (iii) a cleavage site of a further type IIs restriction endonuclease recognition site followed by the recognition site of said cleavage site; the cleavage sites of the type IIs restriction endonuclease recognition sites of item (iii) of entry DNAs 1 to n?1 are complementary to the cleavage sites of the type IIs restriction endonuclease recognition sites of item (i) of entry DNAs 2 to n, respectively; the cleavage site of the type IIs restriction endonuclease recognition site of item (iii) of entry DNA n is complementary to the cleavage site of

Abstract: Disclosed herein are genetically modified microorganisms and related methods for enhanced utilization of oligosaccharides and improved productivity of compounds derived from the metabolism of the oligosaccharides. The microorganisms described herein have altered activities of plasma membrane ATPase protein (PMA1) and/or one or more extracellular glucose sensors, namely, sucrose non-fermenting protein (SNF3), restores glucose transport protein (RGT2), and G protein-coupled receptor 1 protein (GPR1). These genetic modifications provide the microorganisms an increased ability to utilize an oligosaccharide to produce a compound of interest, particularly, tagatose, 2?-fucosyllactose, and psicose. Methods of culturing the microorganisms in the presence of such oligosaccharides to produce the products of interest are also provided.

Abstract: The invention relates to binary vectors based on compatible and autonomous origins, specifically based on the pBBR1 and RK2 replication origins. These binary vectors are useful for having a wide range of hosts, for their maintenance in Agrobacterium sp. and Escherichia coli, and as a new tool for plant synthetic biology as well as a flexible framework for assembly, transfer and characterization of multiple DNA elements. The binary vectors disclosed are small, preferably less than 3.8 kb in size, stable, include an origin compatible with the most commonly used binary T-DNA vectors, comply with current standards for plant synthetic biology, and allow the administration of multiple T-DNA cassettes by means of the multiplexing of the vectors. The present invention also relates to methods for transferring and expressing nucleic acid sequences using said binary vectors, and to the uses of the same.

Abstract: Recombinant DNA constructs, for use in plants and plant cells, have site-specific recombination sites that allow assessing phenotypes and modes of action by over expression or suppression of endogenous genes. In an aspect, a single DNA construct can be switched between over expression and suppression by the action of a recombinase such as the Cre recombinase on constructs having lox recombination sites. Other useful recombination systems include the Flp/frt system, the R/Rs system, the Dre/rox system, and the GIN/gix system.

Abstract: Plant metabolism and alkaloid levels can be regulated by transcription factors that regulate the nicotinic alkaloid biosynthetic pathway. In one embodiment, the disclosure provides a transcription factor that positively regulates alkaloid biosynthesis, such as nicotine biosynthesis. In particular, the present disclosure provides methods for the inhibition of Nicotiana benthamiana auxin response factor 1 (NbTF1) to reduce alkaloid biosynthesis in plants.

Abstract: Autotrophic nitrogen fixation genes and an autotrophic nitrogenase expression cassette for plants and uses thereof are disclosed. Nitrogenase related genes of nitrogen fixation gene cluster from Paenibacillus sp. are specifically optimized by plant expression patterns through synthetic biology, to obtain autotrophic nitrogen fixation genes, which are then constructed into plant constitutive expression units. The expression units are assembled in a plant expression vector by isocaudarner cloning method and transformed into plants, thereby realizing autotrophic nitrogen fixation of the plants.

Abstract: A transgenic plant which exhibits a growth capacity which is enhanced compared to that of a host plant, and has a chimeric protein of a peptide containing an amino acid sequence derived from a motor domain of myosin XI of a donor plant 1, which is a plant species other than the host plant, and a peptide containing an amino acid sequence derived from a domain other than the motor domain of myosin XI of a donor plant 2, which is the host plant or a plant species other than the host plant, the transgenic plant being characterized in that the motor domain loop 2 region has EEPKQGGKGGGKSSFSSIG or EEPKQGGGKGGSKSSFSSIG, and in addition to these sequences, has an amino acid sequence in which one to six amino acids have been deleted, replaced or added.

Abstract: A more efficient breeding against Cercospora leaf spot disease, or the development of new resistant lines, is enabled via the provision of the Cercospora resistance-mediating gene according to the invention; in particular, a dominant resistance effect in the target plant is evoked by the property of the identified gene alone. The Cercospora resistance-mediating gene, and embodiments of the present invention that are described in the preceding, offer additional applications, e.g., the use of the resistant gene allele in cis-genetic or trans-genetic approaches, with the goal of developing new resistant cultivars.

Abstract: Orthotospovirus virions travel through the thrips foregut and enter midgut epithelial cells through the interaction between virus glycoproteins and cellular receptors with several protein motifs thought to be involved in the interaction. Single, double and triple mutant polypeptides in the soybean vein necrosis virus (SVNV)/Neohydatothrips variabilis system are provided herein and several are shown to block viral transmission from the thrips to the soybean plants. Methods for inhibiting viral transmission using these polypeptides or constructs comprising polynucleotides encoding peptides are also provided herein.

Abstract: Provided herein are compositions and methods for packaging a recombinant adeno-associated vims (rAAV) particle comprising using inverted terminal repeats (ITRs) and rep genes of different serotypes and/or using chimeric rep genes.

Abstract: Provided is a method of inserting a polynucleotide sequence into a genome of a cell. The method comprises: generating a double-strand break at a target site of the genome; and introducing into the cell a virus. The virus comprises a nucleic acid comprising the polynucleotide sequence to be inserted or the complementary sequence thereof. The nucleic acid does not comprise a homologous arm or comprises very short (5˜25 bp) homologous arms corresponding to the target site. Also provided herein is a composition for inserting a polynucleotide sequence into a genome of a cell. The composition comprises a site-specific nuclease capable of generating a DNA double-strand break at a target site of the genome and a virus comprising a nucleic acid comprising the polynucleotide sequence or the complementary sequence thereof.

Abstract: The present invention provides a recombinant sequence information of a key host factor ANP32A/B which is necessary for the replication of influenza virus in a host. More specifically, the present invention relates to a 129-130 motif and a 149 site of the host factor ANP32A/B protein, which are key active sites for exerting its ability to promote the replication of influenza virus, and are also potential targeting sites of anti-influenza drugs.

Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.

Abstract: Methods, compositions, and systems for propagation and fermentation, particularly large scale operations for production of ethanol and dried distiller's grain are provided. Addition of Z. mobilis to propagation and/or fermentation decreases lactic acid bacterial contamination.

Abstract: Methods for the preparation of bio-based malonic acid and diester derivatives of malonic acid are provided. For example, a dialkyl malonate may be prepared by the steps of (i) separating calcium malonate crystals from a fermentation broth; (ii) obtaining dissolved malonic acid; (iii) crystallizing the dissolved malonic acid; and (iv) performing esterification to obtain the dialkyl malonate. The disclosed methods produce diester derivatives of malonic acid with fewer impurities, which is useful for many industrial processes. The diester derivatives of malonic acid can be purified from existing sources of malonic acid, or from malonic acid made from a renewable carbon source.

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 methods of synthesizing long-chain polyunsaturated fatty acids, especially eicosapentaenoic acid, docosapentaenoic acid and docosahexaenoic acid, in recombinant cells such as yeast or plant cells. Also provided are recombinant cells or plants which produce long-chain polyunsaturated fatty acids. Furthermore, the present invention relates to a group of new enzymes which possess desaturase or elongase activity that can be used in methods of synthesizing long-chain polyunsaturated fatty acids.

Abstract: This invention relates to the bioproduction of substituted or unsubstituted phenylacetaldehyde, 2-phenylethanol, phenylacetic acid or phenylethylamine by subjecting a starting material comprising glucose, L-phenylalanine, substituted L-phenylalanine, styrene or substituted styrene to a plurality of enzyme catalyzed chemical transformations in a one-pot reaction system, using recombinant microbial cells overexpressing the enzymes. To produce phenylacetaldehyde from styrene, the cells are modified to overexpress styrene monooxygenase (SMO) and styrene oxide isomerase (SOI). To produce phenylacetic acid from styrene, SMO, SOI and aldehyde dehydrogenase are overexpressed. Alternatively, to produce 2-phenylethanol, SMO, SOI and aldehyde reductase or alcohol dehydrogenase are overexpressed, while to produce phenylethylamine, SMO, SOI and transaminase are overexpressed.

Abstract: An improved dry grind system and method for producing a sugar stream from grains or similar carbohydrate sources and/or residues, such as for biofuel production. In particular, a sugar/carbohydrate stream, which includes a desired Dextrose Equivalent (DE) where DE describes the degree of conversion of starch to dextrose (aka glucose) and/or has had removed therefrom an undesirable amount of unfermentable components, can be produced after saccharification and prior to fermentation (or other sugar conversion process), with such sugar stream being available for biofuel production, e.g., alcohol production, or other processes. In addition, the systems and methods also can involve the removal of certain grain components, e.g., corn kernel components, including protein, oil and/or fiber, prior to fermentation or other conversion systems. In other words, sugar stream production and/or grain component separation occurs on the front end of the system and method.

Abstract: The present invention relates to a method for producing a food product comprising hydrolysed starch, as well as to products obtainable by the method. The method has the advantage of reducing the amount of sugar (i.e. maltose) produced by hydrolysis as compared to conventional methods of starch hydrolysis and present the additional advantage of providing good processability for the food product.

Abstract: Embodiments of the present disclosure involve systems and methods that inhibit the production of lactic acid during propagation of yeast and/or during hydrolysis of cellulose by including a sufficient amount of dissolved oxygen.

Abstract: The invention relates to a plasmid, a DNA assembly method and its application recombinant strain. The plasmid has single adjacent Type IIP and Type IIS RE recognition sites. The plasmid combines the properties of Type IIP and Type IIS REs to achieve recursive cycling, SCAR-free and repeat sequence assembly.

Abstract: The present invention relates to methods of upregulating the high mannose glycoform content of a recombinant protein during a mammalian cell culture by manipulating the mannose to total hexose ratio in the cell culture media formulation.

Abstract: The present disclosure relates to approaches for assessing a sample or the presence of microorganisms. The sample, in certain implementations may be assessed for one or both of absence of microorganisms (sterility) and/or for concentration of said organisms (bio-burden). sample partition device may be employed that partitions the sample input volume into multiple discrete measurement zones with little or no loss of sample (e.g., zero-loss) and with little operator involvement, thereby reducing operator- and environment-based false positives.

Abstract: In certain aspects, provided herein are methods and kits for detecting the presence of C. difficile in a biological sample. Also provided herein are methods of selecting of identifying a subject that would benefit from C. difficile treatment.

Abstract: A rapid assay for determining the presence of bacteria in a sample, such as a contaminated food sample, is disclosed. The assay comprises contacting the sample with a bacteria-specific ligand associated with a substrate, wherein bacteria present in the sample bind the ligand; contacting the bound bacteria with a detection agent; detecting the presence of bacteria in the sample by measuring the quantity of detection agent associated with the sample.

Abstract: The invention relates to a method for the identification of a first microorganism potentially secreting an effector compound, said first microorganism thereby having either i. an inhibitory effect on the cell division activity of a second microorganism or ii. an enhancing effect on the cell division activity of a second microorganism, the method comprising: a. providing a cell from a first microorganism which potentially produces an effector compound of interest and a cell from a second detector microorganism; b. introducing both cells into a microdroplet for incubation; c. introducing the microdroplet into a microfluidic system; d. analyzing in said microfluidic system the cell of the second microorganism for the exhibition of an enhanced growth effect or the exhibition of an inhibited growth effect stemming from said effector compound. The invention also relates to a microorganism or effector compound identified by the method according to the invention.

Abstract: The present invention generally relates to a combination of molecular barcoding and emulsion-based microfluidics to isolate, lyse, barcode, and prepare nucleic acids from individual cells in a high-throughput manner.

Abstract: The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5? to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5? flap containing one or more nucleotides at its 3? end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribo

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: The invention provides methods for determining the MSI status of a patient by liquid biopsy with sample preparation using hybrid capture and non-unique barcodes. In certain aspects, the invention provides a method of detecting microsatellite instability (MSI). The method includes obtaining cell-free DNA (cfDNA) from a sample of blood or plasma from a patient and sequencing portions of the cfDNA to obtain sequences of a plurality of tracts of nucleotide repeats in the cfDNA. A report is provided describing an MSI status in the patient when a distribution of lengths of the plurality of tracts has peaks that deviate significantly from peaks in a reference distribution.

Abstract: The invention relates to a method for analysing ribonucleic acid (RNA) interactions comprising: a) cross-linking base-paired nucleotides of at least one RNA molecule and/or at least one pair of RNA molecules using a tagged, reversible cross-linking agent (preferably tagged-psoralen) under ultraviolet irradiation; b) fragmenting the said cross-linked RNA molecule(s); c) using said tag to extract said cross-linked RNA fragment(s); d) ligating the said cross-linked RNA fragment(s) to produce cross-linked ligated RNA chimera(s); e) reversing the cross-linking of the said agent to the said RNA molecule(s); f) preparing a sequence library by sequencing the ligated RNA chimera molecule(s) or pair(s); and g) analysing the sequence library to determine RNA interactions. Also disclosed is a method of studying a subject by analysing RNA interactions and attributing them to a clinical picture, or a drug discovery method by attributing an efficacy score to the drug based upon determined RNA interactions.

Abstract: Embodiments of the present disclosure relate to cyclooctatetraene containing dyes and their uses as fluorescent labels. Also provided are composition containing cyclooctatetraene. The dyes and compositions may be used in various biological applications, such as nucleic acid sequencing.

Abstract: The invention relates to mutant forms of CsgG. The invention also relates to analyte detection and characterisation using CsgG.

Abstract: A method of genotyping includes applying a sample solution including a plurality of copies of a sample polynucleotide to an array of sensors. The sample polynucleotide includes a region associated with an allele. The method further includes measuring using a plurality of sensors of the array of sensors a characteristic of the region of the plurality of copies of the sample polynucleotide and determining using a computational circuitry and the measured characteristics a statistical value indicative of the allele.

Abstract: Provided is a method of analyzing microhaplotypes by using a next generation sequencing (NGS). The method of analyzing microhaplotypes by using the NGS includes: (a) performing a multiplex PCR for simultaneously amplifying the microhaplotypes; (b) performing an indexing PCR by using a product of the multiplex PCR; and (c) performing the NGS by using a product of the indexing PCR.

Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.

Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.

Abstract: The present invention relates to a method, in particular an in vitro method, for identifying PD1+ cells, comprising analyzing the methylation status of at least one CpG position in the mammalian gene region for Programmed cell death 1 (PDCD1), wherein a demethylation or lack of methylation of said gene region is indicative for a PD1+ cell, when compared to a non-PD1+ cell. The analyses according to the invention can identify PD1+ cells on an epigenetic level and distinguish them from all other cells in complex samples, such as, for example, other blood or immune cells. The present invention furthermore provides an improved method for quantifying PD1+ cells, in particular in complex samples. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue.

Abstract: Shortened telomeres are diagnostic of genetic predisposition to cardiomyopathies, e.g. those related to defects in structural proteins expressed in cardiomyocytes.

Abstract: The present invention relates to new methods for diagnosing a pregnancy-associated disorder by analyzing fetal DNA present in the mother's blood. More specifically, this invention relies on the discovery that the maspin gene is differentially methylated in fetal DNA and in maternal DNA and provides these new diagnostic methods, which distinguish fetal DNA from maternal DNA and detect prenatal disorders based on abnormalities in fetal DNA level and methylation status.

Abstract: Methods and compositions disclosed herein generally relate to methods of improving clinical and economic outcomes to address adverse effects related to anesthesia, analgesics, opioids, and inadequate pain relief. Embodiments of the invention relate to the association between genes, specific polymorphisms of genes, and non-genetic factors with inadequate pain relief and anesthesia-, analgesic, and/or opioid-related adverse effects. Embodiments of the invention can be used to determine and manage patient risk factors for development of adverse perioperative effects and can allow for personalized anesthesia and pain management for improvement of pain control and reduction of anesthesia-, analgesic-, and opioid-related adverse outcomes. These methods and compositions apply to non-surgical pain management with opioids.

Abstract: The present invention relates to methods and compositions for reducing the risk of cancer relapse in a subject who has received cancer treatment. It is based, at least in part, on the discovery that a restricted fraction of the gut microbiota, including the bacteria Streptococcus anginosus, Parvimonas micra, Acidaminococcus intestini, Eubacterium limosum, Clostridium glycyrrhizinilyticum, Desulfosporosinus lacus, Eubacterium biforme, Anaerofustis stercorihominis, Pseudoramibacter alactolyticus, Peptococcus niger, Armatimonas rosea, Saccharofermentans acetigenes, Finegoldia magna, Levyella massiliensis, Gallicola barnesae, Murdochiella asaccharolytica, and Eubacterium brachy are associated with a reduced risk of cancer relapse.

Abstract: One variation of a pathogen detection system includes an air sampler and a cartridge. The air sampler includes: a housing defining an inlet and an outlet; a tunnel arranged within the housing and extending between the inlet and the outlet; a charge electrode arranged within the tunnel proximal the inlet; a cartridge receptacle arranged proximal the outlet and comprising a cartridge terminal; and a power supply configured to drive a voltage between the charge electrode and the cartridge terminal. The cartridge includes: a substrate; a collector plate arranged on the substrate and configured to collect charged bioaerosols moving through the tunnel; and a connector configured to transiently engage the cartridge receptacle to locate the substrate and the collector plate within the tunnel and electrically couple the collector plate to the cartridge terminal.