Abstract: Provided herein are compositions and methods for the inhibition of endothelial cell kinesin light chain 1, variant 1 (KLC1C) expression and/or activity, and treatment or prevention of inflammation therewith.

Abstract: The invention relates to double-stranded ribonucleic acid (dsRNA) targeting a PROC gene, and methods of using the dsRNA to inhibit expression of PROC.

Abstract: The invention provides modulators of human cancer and tumor metastasis in particular. More specifically the present disclosure relates to modulators of SKAI1BC, an antisense long non-coding RNA which was found to be an epigenetic suppressor of the metastasis suppressor gene KAI1/CD82, compositions, methods and uses thereof for decreasing metastasis, invasion and possibly also proliferation of cancer cells.

Abstract: Provided herein are methods, compounds, and compositions for reducing expression of an ANGPTL3 mRNA and protein in an animal. Also provided herein are methods, compounds, and compositions for reducing lipids and/or glucose in an animal. Such methods, compounds, and compositions are useful to treat, prevent, delay, or ameliorate any one or more of cardiovascular disease and/or metabolic disease, or a symptom thereof, in an individual in need thereof.

Abstract: The present invention relates to an asymmetric siRNA which inhibits an expression of male pattern hair loss target genes and a use thereof and, more particularly, to an asymmetric siRNA which inhibits an expression of 3-oxo-5-alpha-steroid-4-dehydrogenase 1 (SRD5A1) gene, 3-oxo-5-alpha-steroid-4-dehydrogenase 2 (SRD5A2) gene or androgen receptor (AR) gene, and a composition for prevention or treatment of hair loss comprising the asymmetric siRNA.

Abstract: Aspects of the disclosure relate to methods and compositions for treating retinitis pigmentosa. In some aspects, the disclosure provides compositions and methods for delivering an interfering nucleic acid (for example an interfering RNA) to a subject in order to reduce expression of one or both alleles of an endogenous rho gene (for example a mutant rho allele associated with retinitis pigmentosa) in the subject. In some embodiments, a replacement rho gene that is resistant to the interfering nucleic acid also is delivered to the subject.

Abstract: The present invention includes compositions and methods for treating an autoimmune disorder or a cancer in a subject in need thereof, the method comprising: administering an effective amount of a composition comprising an oligonucleotide that specifically binds a complementary sequence of the Interleukin-7 receptor (IL7R) pre-mRNA that influences splicing of exon 6, wherein the SM-ASO increases or decreases inclusion of exon 6 in IL7R pre-mRNAs and respectively decreases or increases expression of the soluble isoform of IL7R (sIL7R). In certain embodiments, the oligonucleotide is an antisense oligonucleotide (ASO), or a splice-modulating antisense oligonucleotide (SM-ASO).

Abstract: The present application discloses genetically modified yeast cells comprising an active 3-HP fermentation pathway, and the use of these cells to produce 3-HP.

Abstract: This invention relates to the expression a DA1 protein with a mutation that disrupts or inactivates the LIM domain or the LIM-like domain within cells of a plant. This may increase the yield or enhance a yield-related trait of the plant. Methods, plants and plant cells are provide.

Abstract: Described are methods and materials for the genetic modification of plants by specific gene targeting and precise editing of nucleic acid sequences in a plant. The methods and materials provided herein enable one to edit the plant genome by design to control the expression of endogenous genes and/or control the transmission and expression of transgenic traits. Provided are also methods of producing plants having a desirable agronomic trait by crossing a transgenic plant expressing a gRNA with a plant expressing a Cas enzyme, and selecting a progeny plant having the desirable agronomic trait or a seed thereof.

Abstract: Compositions having pesticidal activity and methods for their use are provided. Compositions include isolated and recombinant polypeptides having pesticidal activity, recombinant and synthetic nucleic acid molecules encoding the polypeptides, DNA constructs and vectors comprising the nucleic acid molecules, host cells comprising the vectors, and antibodies to the polypeptides. Polynucleotide sequences encoding the polypeptides can be used in DNA constructs or expression cassettes for transformation and expression in organisms of interest. The compositions and methods provided are useful for producing organisms with enhanced pest resistance or tolerance. Transgenic plants and seeds comprising a nucleotide sequence that encodes a pesticidal protein of the invention are also provided. Such plants are resistant to insects and other pests. Methods are provided for producing the various polypeptides disclosed herein, and for using those polypeptides for controlling or killing a pest.

Abstract: A Thy1 gene promoter specifically expressed in neurons and a recombinant vector including the Thy1 gene promoter are provided. The Thy1 gene promoter may be utilized to regulate an expression of a target gene in preparation of an animal model similar to a human.

Abstract: Provided herein are variant adeno-associated virus (AAV) capsid proteins having one or more modifications in amino acid sequence relative to a parental AAV capsid protein, which, when present in an AAV virion, confer increased infectivity of one or more types of muscle cells as compared to the infectivity of the muscle cells by an AAV virion comprising the unmodified parental AAV capsid protein. Also provided are recombinant AAV virions and pharmaceutical compositions thereof comprising a variant AAV capsid protein as described herein, methods of making these rAAV capsid proteins and virions, and methods for using these rAAV capsid proteins and virions in research and in clinical practice, for example in, e.g., the delivery of nucleic acid sequences to one or more muscle cells for the treatment of muscle disorders and diseases.

Abstract: The present invention relates to the field of molecular biology and cell biology. More specifically, the present invention relates to a CRISPR-CAS system for a yeast host cell.

Abstract: The present disclosure provides modified site-directed modifying polypeptides, and ribonucleoproteins comprising the modified polypeptides. The modified site-directed modifying polypeptides are modified for passive entry into target cells. The modified site-directed modifying polypeptides are useful in a variety of methods for target nucleic acid modification, which methods are also provided.

Abstract: Genetically modified cells that are compatible with multiple subjects, e.g., universal donor cells, and methods of generating said genetic modified cells are provided herein. The universal donor cells comprise at least one genetic modification within or near at least one gene that encodes a survival factor, wherein the genetic modification comprises an insertion of a polynucleotide encoding a tolerogenic factor. The universal donor cells may further comprise at least one genetic modification within or near a gene that encodes one or more MHC-I or MHC-II human leukocyte antigens or a component or a transcriptional regulator of a MHC-I or MHC-II complex, wherein said genetic modification comprises an insertion of a polynucleotide encoding a second tolerogenic factor.

Abstract: Genetically modified cells that are compatible with multiple subjects, e.g., universal donor cells, and methods of generating said genetic modified cells are provided herein. The universal donor cells comprise at least one genetic modification within or near at least one gene that encodes a survival factor, wherein the genetic modification comprises an insertion of a polynucleotide encoding a tolerogenic factor. The universal donor cells may further comprise at least one genetic modification within or near a gene that encodes one or more MHC-I or MHC-II human leukocyte antigens or a component or a transcriptional regulator of a MHC-I or MHC-II complex, wherein said genetic modification comprises an insertion of a polynucleotide encoding a second tolerogenic factor.

Abstract: In one aspect, the present invention provides methods for preparing a fermentation product. The methods include pre-treating a mixture of biomass and ionic liquid, wherein the ionic liquid comprises a choline cation and the biomass comprises polysaccharide and lignin. The methods further include forming hydrolysates from the introduction of glycoside hydrolase to the pre-treated mixture at conditions sufficient to produce a sugar composition mixture for fermentation steps. The present invention provides methods for loading biomass mixtures in a batch-fed process, wherein the biomass slurries can be loaded into water or a concentrated sugar composition for hydrolysate production. The methods can be performed in a one-pot process, wherein the ionic liquids are present in the mixtures throughout each step. Aspects of the invention provide compositions of sugar composition mixtures and fermentation product mixtures.

Abstract: The disclosure relates to a method for fermentation integrated with separation and purification of acetone, butanol, and ethanol (ABE) or butanol alone, comprising the following steps: 1) obtaining ABE by fermentation using an acetone-butanol-producing bacterium or obtaining butanol using a butanol-producing bacterium; 2) using a “vapor-stripping-vapor-permeation” method (briefly VSVP) for online separation and purification of ABE or purifying butanol from the fermentation broth; wherein the VSVP method comprises the following steps: introducing a gas bubble into the fermentation broth comprising active cells for fermentation to vaporize ABE or Butanol; subjecting the gas along with the vaporized ABE or Butanol to a membrane separation unit to pass through the membrane; recovering ABE or Butanol, or subjecting ABE or Butanol to a next separation device.

Abstract: A method comprising a series of selective extraction techniques for the parallel production of biodiesel and isolation of several valuable co-products including an alkenone hydrocarbon mixture of the kerosene/jet fuel range (primarily C10-, C12-, and C17-hydrocarbons) and fucoxanthin, a high-valued carotenoid, from the marine alkenone-producing microalgae Isochrysis.

Abstract: The present invention relates to the preparation of amines from aldehydes and ketones by reductive amination with enzymes having a reductive aminase activity on aldehydes and ketones devoid of any carboxyl group gamma of the carbonyl group. The invention also relates to the enzymes per se and their uses in biocatalysis. The enzymes are derived from Mycobacterium smegmatis and vaccae, Cystobacter fuscus, Microbacterium sp. and Aminomonas paucivorans.

Abstract: The invention provides microorganisms genetically modified to co-overexpress a carbohydrate binding module and lysine decarboxylase polypeptides in a mesophilic host to enhance the production of lysine derivatives by the microorganism, method of generating such microorganism, and methods of producing lysine derivatives using the genetically modified microorganisms.

Abstract: The present invention relates to a novel method for purifying 3,6-anhydro-L-galactose by using microorganisms and provides an effect of improving the production yield of 3,6-anhydro-L-galactose by using microorganisms during purification after enzymatic hydrolysis of agarose or agar.

Abstract: The invention relates, in general, to methods of processing lignocellulosic biomass to fermentable sugars and to methods that rely on hydrothermal pretreatment. Xylose monomer yields comparable to those achieved using two-stage pretreatments can be achieved from soft lignocellulosic biomass feedstocks by pretreating to very low severity in a single-stage pressurized hydrothermal pretreatment, followed by enzymatic hydrolysis to release xylose retained in the solid state. In some embodiments, pretreated biomass is separated into a solid fraction and a liquid fraction, the solid fraction subjected to enzymatic hydrolysis, and the separated liquid fraction subsequently mixed with the hydrolysed solid fraction.

Abstract: In one aspect, the present invention provides a method for preparing a sugar composition. The method includes: forming a mixture including polysaccharide biomass and an ionic liquid solution, wherein the ionic liquid solution contains water and an ionic liquid, and wherein the ionic liquid contains a dicarboxylic acid anion and a cation. The pH of the mixture is greater than or equal to about 10, and the molar ratio of the dicarboxylic acid anion to the cation is at least about 1:2. The method further includes: maintaining the mixture under conditions sufficient to dissolve at least a portion of the polysaccharide present in the polysaccharide biomass; reducing the pH of the mixture containing the dissolved polysaccharide to at least about 7; adding at least one glycoside hydrolase to the mixture having the reduced pH.

Abstract: The present invention discloses a process for producing N-acetyl-D-glucosamine and D-glucosamine salts by microbial fermentation. The invention includes a method to produce N-acetyl-D-glucosamine and/or D-glucosamine salts with higher efficiency and higher yield by increasing the effect of N-acetyl-D-aminomannose-6-phosphate epimerase in microorganisms.

Abstract: Disclosed herein are methods for multiple stage isothermal amplification of nucleic acid comprising a first substantially isothermal amplification reaction on the nucleic acid to generate a first amplification product and at least one substantially isothermal amplification reaction on the first amplification product to generate at least one second amplification product in an amount sufficient for recovery, testing, or characterization.

Abstract: The present invention is directed to methods and compositions for adding tails of specific lengths to a substrate polynucleotide. The invention also contemplates methods and compositions for immobilization of tailed substrates to a solid support. The disclosure contemplates that the attenuator molecule is any biomolecule that associates with a tail sequence added to a substrate polynucleotide and controls the addition of a tail sequence to the 3? end of the substrate polynucleotide. The sequence that is added to the substrate polynucleotide is referred to herein as a tail sequence, or simply a tail, and the process of adding a nucleotide to a substrate polynucleotide is referred to herein as tailing.

Abstract: The present invention relates to methods and compositions for modulating glycosylation profile, such as the galactosylation profile, of recombinant proteins expressed by mammalian host cells during the cell culture process by supplementing cell culture media with a peracetyl galactose.

Abstract: Provided is a device for determining the live/dead bacterial state, with which it is possible to ascertain the accurate state of live bacteria/dead bacteria via a captured image in a relatively easy operation with which ascertaining the state of a bacterial cell is more accurate than conventional methods. This device for determining the live/dead bacterial state comprises: a case body in which a measurement mechanism is housed; an opening/closing lid body that allows a fungus base insertion port formed in the case body to be opened and closed; and the measurement mechanism, which is housed in the case body and is configured to measure the number of bacteria.

Abstract: Hybrid gas vesicle gene cluster (GVGC) configured for expression in a prokaryotic host are described comprising gas vesicle assembly (GVA) genes native to a GVA prokaryotic species and capable of being expressed in a functional form in the prokaryotic host, and one or more gas vesicle structural (GVS) genes native to one or more GVS prokaryotic species, at least one of the one or more GVS prokaryotic species different from the GVA prokaryotic species, and related gas vesicle reporting (GVR) genetic circuits, genetic, vectors, engineered cells, and related compositions methods and systems to produce GVs, hybrid GVGC and/or image a target site.

Abstract: The instant invention provides workflows for the design and characterization of mechanism-based sirtuin modulating compounds, including new or improved sirtuin activating compounds. Workflows for the design of mechanism-based sirtuin activating compounds are provided, based on conditions that must be satisfied by activators if they are to exploit the common catalytic mechanism of all sirtuin enzymes and hence increase catalytic efficiency for any sirtuin and any substrate.

Abstract: The invention is directed to methods for identifying one or more introns of a gene that are rapidly processed from a nascent RNA molecule transcribed from the gene, which allows for the detection of allele-specific expression of a gene in a single cell.

Abstract: A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.

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 amount effective to denature double-stranded nucleotide sequences.

Abstract: In one aspect, the present invention relates to a method for obtaining structural information about an encoded molecule. The encoded molecule may be produced by a reaction of a plurality of chemical entities and may be capable of being connected to an identifier oligonucleotide containing codons informative of the identity of the chemical entities which have participated in the formation of the encoded molecule. In a certain embodiment, primers are designed complementary to the codons appearing on the identifier oligonucleotide, and the presence, absence or relative abundance of a codon is evaluated by mixing a primer with the identifier oligonucleotide in the presence of a polymerase and substrate (deoxy)ribonucleotide triphosphates and measuring the extension reaction. In another aspect, the invention provides a method for selecting compounds which binds to a target.

Abstract: Disclosed are compositions, methods and kits for determining the presence, absence, amount, copy number, or other characteristics of one or more polynucleotide sequences in two or more samples and use thereof in genotyping, evaluation of copy number variation, expression analysis, determination of splice variants and fusion genes, and other genetic analyses.

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: An article for forming emulsion droplets includes a body having an inlet port, an outlet, and a reservoir configured to receive both an aqueous phase and an organic phase through the inlet port. By applying a force to the contents of the reservoir, an aqueous phase stream and a separate organic phase stream from the reservoir are generated and later combined to form emulsion droplets which are dispensed through the outlet, typically into a receptacle for analysis or further processing.

Abstract: The technology relates in part to methods and compositions for isothermal amplification of nucleic acids.

Abstract: Methods of volumetric imaging of a three-dimensional matrix of nucleic acids within a cell is provided. An automated apparatus for sequencing and volumetric imaging of a three-dimensional matrix of nucleic acids is provided.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: Aspects of the invention include methods for preparing an enriched sequencing library. In some embodiments, the methods involve preparing a sequencing library that is enriched for AT-rich sequences. In certain embodiments, the methods involve determining a presence or an absence of cancer, determining a cancer stage, monitoring cancer progression, and/or determining a cancer classification in a subject by analyzing an enriched sequencing library.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

Abstract: Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: The invention provides methods and compositions for hybridizing at least one molecule to a target. The invention may, for example, utilize a of cyclic and/or non-cyclic solvent that is non-toxic and may eliminate or reduce the amount of formamide in the hybridization composition.

Abstract: A method for assessing whether a test substance or treatment is potentially neuroprotective or anti-oxidant, the method comprising the steps of exposing a cell to the test substance or treatment assessing the TSPO level in the cell, wherein a substance or treatment is considered to be potentially anti-oxidant and/or neuroprotective if the TSPO level is decreased. The method may comprise the step of assessing the level of mitophagy in the cell, wherein a substance or treatment is considered to be anti-oxidant or neuroprotective if the level or induction of mitophagy is increased and the TSPO level is decreased.

Abstract: Provided herein is technology for neoplasia screening, and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of cancer, in particular, colorectal cancer.

Abstract: One aspect of the invention is a method for amplifying alpha globin genes HBA1, HBA2 and HBA12 in a single PCR tube to determine an HBA genotype of a subject. This method employs five primers selected to accurate and sensitively identify the HBA1, HBA2, and HBA12, a gene found at a higher frequency in citizens of Saudi Arabia, by accurately annealing to nucleic acids in a biological sample and simultaneously amplifying sequences encoding the alpha globin genes. This invention includes a procedure and required reagents for the amplification of alpha globin genes in a single PCR tube.