Abstract: This invention generally relates to the field of somatic gene therapy. The invention provides a nucleic acid construct comprising a transgene encoding a therapeutic protein, a tetracycline-responsive aptazyme sequence, and inverted terminal repeats (ITRs). The nucleic acid construct can be transferred to a subject in need thereof in the form of a viral vector, in particular an adeno-associated virus (AAV) vector. The Tet-responsive aptazyme sequence allows for a tightly controlled expression of the transgene in the subject, thereby avoiding toxic side effects. The nucleic acid construct and the viral vectors comprising same are particularly useful in the treatment of proliferative diseases like cancer.

Abstract: A group of viral vectors including: first viral vector, wherein first viral vector carries first nucleic acid molecule, and the first nucleic acid molecule encodes envelope protein; second viral vector, wherein second viral vector carries second nucleic acid molecule, the second nucleic acid molecule encodes fusion protein, the fusion protein includes single-chain antibody and C-terminal domain of envelope protein, the C-terminal domain of envelope protein includes transmembrane region and intracellular region of envelope protein, the C-terminus of single-chain antibody connects with N-terminus of C-terminal domain of envelope protein, the single-chain antibody targets a specific antigen; first nucleic acid molecule and second nucleic acid molecule are arranged to express envelope protein and fusion protein, and the envelope protein and the fusion protein are in non-fusion form.

Abstract: The present application relates to the fields of genetics, gene therapy, and molecular biology. More specifically, the present invention relates to an isolated codon-optimized nucleic acid that encodes the FIX (coagulation factor IX) protein, an expression cassette and a vector based thereon, as well as an AAV5 (adeno-associated virus serotype 5)-based recombinant virus for increasing the expression of the FIX gene in target cells, and use thereof.

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: The present disclosure provides rAAV vectors and rAAV virions that specifically express exogenous nucleic acid sequences in CD14+ cells. The rAAV vectors or virions are useful for specifically expressing exogenous nucleic acid sequences encoding, for example, cancer antigens, viral antigens, and/or bacterial antigens in monocytes and dendritic cells. The rAAV transduced CD14+ cells can be used as antigen presenting cells that induce antigen-specific T cell responses. The present disclosure further provides methods producing rAAV virions and methods of immunotherapy.

Abstract: Provided is a pharmaceutical composition for treatment or prevention of macular degeneration and, more particularly, to a recombinant vector carrying a soluble VEGF receptor variant cDNA and a pharmaceutical composition including the same for treatment or prevention of macular degeneration. According to the present disclosure, age-related macular degeneration, which is a representative retinal disease causing blindness in adults, can be effectively treated and a prophylactic effect can be expected.

Abstract: The present disclosure provides adeno-associated virus (AAV) vectors, comprising coevolved capsid variant proteins, pharmaceutical compositions, methods of making, and methods for delivering such to a subject.

Abstract: Disclosed are a composition and method of treating or preventing cardiomyopathy in a human subject. In some embodiments, the method comprises delivering a therapeutic dose of a gene therapy vector to cardiomyocytes of the human subject, wherein the gene therapy vector comprises a nucleic acid sequence encoding for PKP2.

Abstract: The present disclosure provides compositions of matter, methods, systems, and instruments for improved nucleic acid-guided nuclease editing in live cells, wherein the live cells are shifted into a growth-arrested state for editing.

Abstract: Methods and compositions for modulating a target genome are disclosed.

Abstract: Systems and methods for prenylation and recombinant pathways for the production of compounds, cannabinoids, cannabinoid precursors, and other prenylated chemicals in a cell free system. The present invention further includes enzymes and recombinant microorganisms that catalyze the reaction. The compounds, cannabinoids, cannabinoid precursors, and other prenylated chemicals are operable to be substituted with at least one deuterium, at least one tritium, at least one halogen, at least one hydroxyl group, and/or at least one additional isotope.

Abstract: Recombinant Aspergillus genetically modified to increase expression of g8846, renamed herein as aconitic acid exporter (aexA), are provided, which in some examples are also genetically inactivated for an endogenous cis-aconitic acid decarboxylase (cadA) gene. Such recombinant Aspergillus produce more aconitic acid as compared to native Aspergillus. Also provided are methods of using such recombinant Aspergillus to increase production of aconitic acid and other organic acids, such as citric acid, itaconic acid, and 3-hydroxypropionic acid (3-HP).

Abstract: Provided are a recombinant strain with modified gene BBD29_14900, and a method for constructing the same and use thereof, with the production of L-glutamic acid as a specific application. Further provided is a method for introducing a point mutation into the BBD29_14900 gene coding sequence in Corynebacterium or improving the expression thereof. The method can cause a bacterial strain with the mutation to increase the fermentation yield of glutamic acid. The point mutation involves a mutation of the base at position 1114 in the sequence of the BBD29_14900 gene from guanine (G) to adenine (A), and thus a substitution of aspartic acid at position 372 in the coded corresponding amino acid sequence with asparagine.

Abstract: Provided herein are methods for making gamma lactones comprising reacting a carboxylic acid substrate with a heterologous cytochrome P450 (CYP450) protein with carboxylic acid 4-hydroxylase activity.

Abstract: The present disclosure provides MTR kinase polypeptides having improved properties as compared to a naturally occurring wild-type MTR kinase polypeptide including the capability of phosphorylating D-ribose and 5?-D-isobutyrylribose to give alpha-D-ribose-1-phosphate and alpha 5?-D-isobutyrylribose-1-phosphate. Also provided are polynucleotides encoding the MTR kinase polypeptides, host cells capable of expressing the MTR kinase polypeptides, and methods of using the MTR kinase polypeptides to synthesize alpha-D-ribose-1-phosphate and alpha 5?-D-isobutyrylribose-1-phosphate.

Abstract: Described is a method of producing bioproducts by fermentation with a genetically modified cell, as well as to the genetically modified cell used in the method. The cell is genetically modified to produce a bioproduct and is further genetically modified by reducing the expression of at least one endogenous membrane protein encoding gene and/or mutating the expression of the endogenous membrane protein.

Abstract: The present disclosure discloses ?-carrageenase mutant OUC-CglA-DPQQ, which has an amino acid sequence as set forth in SEQ ID NO. 1 and an encoding gene as set forth in SEQ ID NO. 2. The ?-carrageenase mutant OUC-CglA-DPQQ is applied to degradation of carrageenan/preparation of ?-carrageenan oligosaccharides with high polymerization degree. The present disclosure further discloses a method for degrading carrageenan/preparing ?-carrageenan oligosaccharides with high polymerization degree by using the ?-carrageenase mutant OUC-CglA-DPQQ. The ?-carrageenase mutant OUC-CglA-DPQQ of the present disclosure can act on low viscosity carrageenan, and the polymerization degree of final product ?-carrageenan oligosaccharides is 10-20. The ?-carrageenase mutant of the present disclosure is excellent in enzymatic properties and specificity, and has important industrial application value and economic value in the preparation of ?-carrageenan oligosaccharides via an enzyme method.

Abstract: MLX1034 is from Polaribacter sp. Q13, and has the amino acid sequence of the 1,3/1,4-xylanase MLX1034 is listed in SEQ ID NO.1; a nucleotide sequence of the gene is listed in SEQ ID NO.2; the 1,3/1,4-xylanase MLX1034 in the invention is capable of efficiently and specifically degrading 1,3/1,4-xylan and producing xylooligosaccharides with DP values above one; in addition, the physical and chemical properties of the 1,3/1,4-xylanase MLX1034 are stable enough to hydrolyze 1,3/1,4-xylan at room temperature; the 1,3/1,4-xylanase MLX1034 is suitable for the industrial production of red algal xylooligosaccharides at low energy costs.

Abstract: The present disclosure discloses a method for modifying a DNA by utilizing a glycosylase and an oxyamine compound, including the following steps: conducting solid phase synthesis of a DNA strand carrying a non-canonical base; reacting the DNA strand carrying a non-canonical base under the catalysis of the glycosylase which selectively recognizes the non-canonical base, to produce a DNA strand carrying an abasic site; and reacting the DNA strand carrying the abasic site with the oxyamine compound to generate a DNA modified with a chemical functional group. This method can realize diverse site-directed modification of the DNA, can be used to study the base structure-function relationship of a functional DNA, and construct a functional DNA with higher activity. The present method is simple and easy to use, and can reduce the cost and the time required for modification. The modified functional DNA has higher activity and can provide better tool molecules for biotechnology, disease diagnosis and treatment.

Abstract: Methods of preparing highly purified steviol glycosides, particularly rebaudiosides A, D and M are described. The methods include utilizing recombinant microorganisms for converting various staring compositions to target steviol glycosides. In addition, novel steviol glycosides reb D2 and reb M2 are disclosed, as are methods of preparing the same. The highly purified rebaudiosides are useful as non-caloric sweetener in edible and chewable compositions such as any beverages, confectioneries, bakery products, cookies, and chewing gums.

Abstract: Described herein is a low perfusion rate cell culture method for producing recombinant proteins.

Abstract: Disclosed herein are systems, methods and compositions of matter for engineered formate dehydrogenases electrocatalytically driven in reverse to fix CO2 to formate, an electrode interface composed of self-assembled monolayers (SAM), and a nanowire link between the electrode and the enzyme's iron sulfur (FeS) cluster (engineered) to specifically link the iron sulfur cluster to the electrode. Engineering the interface between the enzyme and the electrode enables a high degree of activity and function compared to just an enzyme immobilized on the electrode. This interface enables specific orientational control of the enzyme and allows for separation of the enzyme from the electrode surface to allow retention of its native hydrodynamic radius. The transfer of electrons via the nanowire to the FeS cluster allows the enzyme to utilize its native electron transfer pathways.

Abstract: The present disclosure is based on the discovery that cells enriched with mitochondria are useful for treating diseases and disorders. The present invention provides methods of identifying or detecting such cells enriched with exogenous mitochondria. Specifically, the identification or detection of mitochondria-enriched cells is determined by utilization of a substrate such as tryptamine. This includes determining levels of MonoAmine oxidase A (MAO-A), Mono Amine oxidase-B (MAO-B), glycerol-3-phosphate dehydrogenase or a combination thereof. The present invention also provides kits for the identification or detection of mitochondria-enriched cells.

Abstract: Compositions and methods are provided for simple, instrument-free and sensitive methods that enable rapid, point-of-care detection of nucleic acid molecules of interest. This is based on a surprising discovery that the relative efficiencies of amplification and CRISPR-based cleavage and detection can be tuned to favor amplification until sufficient amplified products are generated to enable detection. Example approaches include design of guide RNA and primers to target nonoptimal PAM sequences, or sequence-engineering Cas nucleases to reduce activities informing a ribonucleoprotein with the guide RNA or binding to or cleaving the substrate nucleic acid.

Abstract: Methodologies to detect off-target mutations induced by the deaminase activity of Base Editing technology.

Abstract: The present disclosure relates to paper microfluidic devices for use in combination with a viewing box assembly for imaging and rapid identification and quantification of target analytes in a fluid sample that is deposited onto the device such that one or more target analytes in the sample react with one or more diagnostic components on the paper, causing a detectable reaction. The reacted microfluidic device may then be placed inside an opaque viewing box having an internal light source and top panel viewing aperture through which the microfluidic device may be imaged using a mobile electronic device and graphical user-interface for purposes of detecting and quantifying the one or more target analytes. In some embodiments, the microfluidic device includes diagnostic paper and abase. In some embodiments, the microfluidic device includes a filter layer on top of diagnostic paper layer.

Abstract: Provided herein are methods and products for detecting analytes in a sample. The analytes may be rare analytes such as biomarkers in a biological sample. These methods make use of nucleic acid nanoswitches that adopt a particular conformation and have a particular length in the presence of an analyte.

Abstract: Methods for making and using reagents and adapters for use in nucleic acid sequencing applications are disclosed herein. In several embodiments, adapters and reagents and the methods of making such adapters and reagents can be used for Duplex Sequencing applications.

Abstract: Some embodiments of the methods and compositions provided herein relate to the selective cleavage of a target nucleic acid. Some such embodiments include the selective cleavage of a target nucleic acid that is associated with a DNA-binding protein or comprises a methylated CpG island, with a recombinant nuclease. In some embodiments, the DNA-binding protein comprises a chromatin protein. Some embodiments also include the enrichment of non-target nucleic acids in a sample by selective cleavage of target nucleic acids in the sample, and removal of the cleaved target nucleic acids from the sample.

Abstract: CRISPNA, a new tool for genome editing and diagnosis. The present invention relates to methods and systems for genome editing and diagnosis, and specifically relates to use of Peptide Nucleic Acids (PNAs) to direct the Cas proteins to their DNA or RNA targets.

Abstract: A method for determining the presence, absence or amount of two or more target polynucleotides in a sample comprising additional components, the method comprising: (i) contacting the sample with a panel of two or more probes under conditions suitable for hybridisation of the target polynucleotides to the probes, wherein: (a) each probe comprises a non-hybridisation region and a hybridisation region that specifically hybridises to one of the target polynucleotides to form a hybridised probe; and (b) the hybridisation region of a probe of the panel comprises one or more non-natural nucleotides; (ii) contacting the sample prepared in step (i) with a transmembrane pore through which a single stranded polynucleotide but not a double stranded polynucleotide can pass and applying a potential difference to the transmembrane pore such that the hybridised probes in the sample interact with the pore; (iii) measuring current blockades having a duration within a defined window, wherein: (a) the one or more non-natu

Abstract: Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.

Abstract: The present disclosure relates in some aspects to methods for manufacturing molecular arrays using a hybrid approach comprising microfluidics-based delivery and photolithography-guided oligonucleotide hybridization and ligation. In particular, the molecular arrays can be used for determining spatial patterns of abundance and/or expression of a biological target in a sample.

Abstract: The present disclosure relates in some aspects to methods and compositions for processes for inverting oligonucleotide molecules in an in situ synthesized array, including reversing the orientation of the oligonucleotide molecules with respect to the array substrate from 3?-immobilized to 5?-immobilized.

Abstract: Provided herein are methods of determining a location of an analyte in a biological sample, and systems for performing these methods. In particular, the methods and systems comprise decreasing the binding events of an analyte from a biological sample to capture probes that surround a biological sample positioned on a substrate.

Abstract: An automated method for performing an assay of the present disclosure can be performed in a microfluidic device that is a lateral flow device having numerous features to ensure correct operation of the device under gravity, such as vent pockets for enabling the flow of sample fluid from one chamber to the next when the vent pocket is unsealed. Each chamber can have a reagent recess proximal to an inlet end of the chamber. A reagent pellet formed in a reagent recess can be effectively mixed with a sample as the sample flows into the chamber. A flexible circuit with patterned metallic electrical components disposed on a heat stable material can be in direct contact with fluid in the chambers and has resistive heating elements aligned with, for example, a chamber for performing an amplification reaction.

Abstract: The present disclosure provides a microfluidic substrate, a microfluidic chip, a method for preparing the microfluidic chip, and a method for using the microfluidic chip. The microfluidic substrate includes a substrate including a plurality of microcavity regions arranged m an array, each of the plurality of microcavity regions includes a first portion and a second portion that are stacked, and the depth of the first portion is x, and the first portion includes a top opening that is circular in shape and has a diameter D, the relationship between the diameter D of the top opening and the depth x is approximately D=2x+y, where the range of x is from 20 microns to 400 microns, and the range of y is from 5 microns to 30 microns.

Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.

Abstract: The technology described herein is directed to methods of determining oligonucleotide sequences, e.g. by enriching target sequences prior to sequencing the sequences.

Abstract: The invention provides a method for detecting KRAS mutations at one or more of codons, said method comprising the steps of: (a) extracting DNA from a biological sample; (b) assaying the DNA via PCR for KRAS mutations at one or more of codons with at least one set of oligonucleotides, wherein the at least one set of oligonucleotides comprises an allele specific forward primer, a reverse primer, a probe and a xenonucleic acid clamp to block amplification of wild type DNA. The xenonucleic acid clamps have aza-aza, thio-aza and oxy-aza chemical functionality.

Abstract: Provided herein is a method of characterising a target polynucleotide as it moves with respect to a nanopore using a motor protein. Also provided are polynucleotide adapters and kits comprising such adapters. The methods, kits and adapters find use in characterising polynucleotides, for example in sequencing.

Abstract: The present disclosure provides a method and systems for processing or analyzing a nucleic acid molecule. A method for processing or analyzing a double-stranded nucleic molecule may comprise providing the double-stranded nucleic acid molecule and a double-stranded adapter. The double-stranded adapter may comprise a nicking site within a sense strand or an anti-sense strand of the double-stranded adapter. The double-stranded adapter may then be coupled to the double-stranded nucleic acid molecule, and the double-stranded nucleic acid molecule coupled to the double-stranded adapter may be circularized to generate a circularized double-stranded nucleic acid molecule.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. The methods and compositions can be used to pair any two sequences originating from a single cell, such as heavy and light chain antibody sequences, alpha and beta chain T-cell receptor sequences, or gamma and delta chain T-cell receptor sequences, for antibody and T-cell receptor discovery, disease and immune diagnostics, and low error sequencing.

Abstract: This invention provides devices for use in various analytical applications including single-molecule analytical reactions. Methods for detecting analytes optically by propagating optical energy by waveguides within a substrate are provided. Analytical devices are provided which have both shallow and deep waveguides in which illumination light is transported through the deep waveguides and coupled into the shallow waveguides. The shallow waveguides provide evanescent field illumination to analytes, such as single-molecule analytes, within nanometer scale wells. Integrated devices including integrated detectors such as CMOS detectors are included.

Abstract: The invention relates to a method for detection of analyte interaction with a channel molecule held in a membrane, comprising the optical detection of a modification in the flux of a signal molecule as it passes through the channel molecule by the action of a membrane potential, wherein the modification in the flux is caused by at least partial blockage of the channel molecule by the analyte. The invention further relates to bilayer arrays, components, methods of manufacture and use.

Abstract: A method for detecting a whole transcriptome RNA structure and the use thereof A method for detecting an intact RNA structure by combining in vivo click chemistry selective 2?-hydroxy acylation and mutation map analysis. Combined with the RNA immunoprecipitation technology, the method is further applied to analyze a RNA structure map of Dicer-bound substrates, and reveals the structural type and characteristics of the Dicer substrates. The method provided for detecting a whole transcriptome RNA structure can also perform complete full-length structure analysis on small RNAs, thereby laying the foundation for the research on the structure and biological functions of RNA molecules in a whole transcriptome in cells.

Abstract: The disclosure provides compositions and methods for characterizing the genome and transcriptome at a single cell level. In some embodiments, the method provides for the characterization of CRISPR editing outcomes and phenotypes, as well as other alterations in polynucleotide sequences, particularly in primary cells.

Abstract: A honeycomb tube with a planar frame defining a fluidic path between a first planar surface and a second planar surface. A fluidic interface is located at one end of the planar frame. The fluidic interface has a fluidic inlet and fluidic outlet. The fluidic path further includes a well chamber having an well-substrate with a plurality of wells. The well chamber is arranged in the planar frame between the first or second surface and the well-substrate.

Abstract: Disclosed are methods for distinguishing subpopulations of cells within a cell population and determining analyte expression in the subpopulations. Herein, subpopulations of cycling and non-cycling cells were identified in a cell population based on expression of a first analyte (e.g., Ki-67). Levels of a second analyte were determined in the cycling cells, exclusive of the non-cycling cells.