Abstract: Polymeric nanoparticles encapsulating inhibitory ribonucleic acids (RNAs) and methods of their manufacture and use are provided. Advantageous properties of the nanoparticles include: 1) high encapsulation efficiency of inhibitory RNAs into the nano articles, 2) small size of the nanoparticles that increases cell internalization, and 3) sustained release of encapsulated inhibitory RNAs by the nanoparticles that allows for administration of an effective amount of inhibitory RNAs to cells or tissues over extended periods of time. Encapsulation efficiency of inhibitory RNAs into the nanoparticles is greatly increased by complexing the inhibitory RNAs to polycations prior to encapsulation. Methods of using the polymeric nanoparticles for treating or inhibiting diseases or disorders are provided.

Abstract: The invention relates to a double-stranded ribonucleic acid (dsRNA) for inhibiting the expression of the PCSK9 gene (PCSK9 gene), comprising an antisense strand having a nucleotide sequence which is less that 30 nucleotides in length, generally 19-25 nucleotides in length, and which is substantially complementary to at least a part of the PCSK9 gene. The invention also relates to a pharmaceutical composition comprising the dsRNA together with a pharmaceutically acceptable carrier and method for treating diseases caused by PCSK9 gene expression.

Abstract: The invention relates to methods for decreasing, inhibiting, preventing, or reducing calcification by inhibiting sortilin 1.

Abstract: Described herein is a method of preventing or treating ocular vascular hyperpermeability including macular edema, in a subject comprising inhibiting Sema3A activity. Also disclosed are compositions and their use for preventing or treating Sema3A-dependent ocular vascular hyperpermeability.

Abstract: Modulators of intracellular chloride concentration for treating down syndrome The present invention relates to a modulator of a chloride transporter for use in the treatment of Down syndrome.

Abstract: The present invention is related to an L nucleic acid that binds to an SDF-1.

Abstract: Disclosed herein are methods, compositions, and kits for high efficiency, site-specific genomic editing of cells.

Abstract: Provided is a separatome-based peptide, polypeptide, and protein expression and purification platform based on the juxtaposition of the binding properties of host cell genomic peptides, polypeptides, and proteins with the characteristics and location of the corresponding genes on the host cell chromosome of E. coli. The separatome-based protein expression and purification platform quantitatively describes and identifies priority deletions, modifications, or inhibitions of certain gene products to increase chromatographic separation efficiency, defined as an increase in column capacity, column selectivity, or both, with emphasis on the former. Moreover, the separatome-based protein expression and purification platform provides a computerized knowledge tool that, given separatome data, and a target recombinant peptide, polypeptide, or protein, intuitively suggests strategies facilitating efficient product purification.

Abstract: The invention provides for 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 eukaryotic cells and methods for selecting specific cells by introducing precise mutations utilizing the CRISPR/Cas system.

Abstract: The present disclosure provides mutant cells for the secretion of proteins and for the degradation of lignocellulosic biomass. Methods for the use of these cells are also provided. Specifically, the utility of combined genetic deletions of ?-glucosidases and the catabolite repressor gene creA/cre-1 for protein secretion in fungal and yeast cells is disclosed.

Abstract: A recombinant micro-organism such as Saccharomyces cerevisiae which produces and excretes into culture medium a stilbenoid metabolite product when grown under stilbenoid production conditions, which expresses in above native levels a ABC transporter which transports said stilbenoid out of said micro-organism cells to the culture medium. The genome of the Saccharomyces cerevisiae produces an auxotrophic phenotype which is compensated by a plasmid which also expresses one or more of said enzymes constituting said metabolic pathway producing said stilbenoid, an expression product of the plasmid is genetically modified to include a ubiquitination tag sequence. Expression of an enzyme participating in catabolism of phenylalanine by the Ehrlich pathway is optionally reduced compared to its native expression level.

Abstract: Use of an isolated Ensifer adhaerens strain OV14 deposited under NCIMB Accession Number 4177, or an isolated variant thereof characterized by a 16S rRNA gene having at least 98.6% sequence homology with SEQUENCE ID NO: 1, as a gene delivery system in the genetic transformation of a plant cell or plant material is described.

Abstract: Compositions and methods for modulating nucleotide sequence expression, particularly for modulating gene expression in plants, are provided. The compositions comprise precursor RNA constructs for the expression of an RNA precursor. The precursor RNA construct comprises a promoter that is expressed in a plant cell driving the expression of a precursor RNA having a microRNA. The miRNA is complementary or partially complementary to a portion of a target gene or nucleotide sequence and function to modulate expression of the target sequence or gene. In this manner, the RNA precursor construct can be designed to modulate expression of any nucleotide sequence of interest, either an endogenous plant gene or alternatively a transgene. Transformed plants, tissues, cells and seeds are also provided.

Abstract: The present invention provides a mutant CD83 promoter comprising the promoter/enhancer regions of human CD83 promoter and being dendritic cell-specific, and the use thereof, specifically for the treatment or prevention of diseases or medical conditions related to malignancy, autoimmunity or prevention of transplant rejections.

Abstract: A circular mRNA molecule possessing features resembling native mammalian mRNA demonstrates improved translation, while retaining the properties of an extremely long half-life inside cells. This circular mRNA is functional inside mammalian cells, being able to compete against native cellular mRNAs for the eukaryotic translation initiation machinery. The invention possesses additional RNA elements compared to a previous invention containing only an IRES element for successful in vitro or in vivo translation.

Abstract: The invention relates to expression systems useful for regulated expression of a gene of interest based on the constitutive expression of the original TetR repressor and the expression of the polynucleotide driven by a constitutive promoter operably linked to an operator sequence for a tetracycline operator sequence. The system can be provided as two different polynucleotides or as an all-in-one vector. The invention also relates to vectors, host cells and viral particles according to the invention as well as to the uses thereof for in vitro and in vivo production of products of interest or for therapy.

Abstract: A nucleic acid comprising a transcription regulation sequence whose transcription is induced by a trans-acting factor of a human immunodeficiency virus and a gene encoding a polypeptide having an endoribonuclease activity specific to single-stranded RNA, wherein the gene is located in such a position that the expression of the gene can be regulated by the transcription regulation sequence; a method for production of a cell showing an inhibited replication of a human immunodeficiency virus therein, the method comprising the step of introducing the nucleic acid into a cell; and a method for treatment or prevention of a human immunodeficiency virus infection.

Abstract: Methods of inserting genes into defined locations in the chromosomal DNA of cultured mammalian cell lines which are subject to gene amplification are disclosed. In particular, sequences of interest (e.g., genes encoding biotherapeutic proteins) are inserted proximal to selectable genes in amplifiable loci, and the transformed cells are subjected to selection to induce co-amplification of the selectable gene and the sequence of interest. The invention also relates to meganucleases, vectors and engineered cell lines necessary for performing the methods, to cell lines resulting from the application of the methods, and use of the cell lines to produce protein products of interest.

Abstract: A process for making ethanol by fermentation comprises the steps fermenting a mash comprising a fermentable sugar with a yeast to form a fermented mash comprising ethanol, separating a yeast concentrate from the fermentation mash, adding a mineral acid to the yeast concentrate to provide an acidified yeast concentrate having a pH between 1.8 and 3.0, adding a peroxycarboxylic acid to the acidified yeast concentrate in an amount of from 5 to 80 ppm by weight to provide a treated yeast concentrate, and fermenting a mash comprising a fermentable sugar with addition of treated yeast concentrate to form a fermented mash comprising ethanol.

Abstract: It is disclosed a continuous process for soaking a ligno-cellulosic biomass stream in an extraction solution comprising water and dissolved water soluble species derived from a previously treated ligno-cellulosic biomass, wherein the soaked ligno-cellulosic biomass stream is optionally rinsed with a rinse solution stream to produce a soaking liquid. The electrical conductivity of the extraction solution and/or the soaking liquid are controlled to a value in a suitable target range by regulating one or more dilution streams. The disclosed process is useful to remove non-ligno-cellulosic water soluble compounds from the ligno-cellulosic biomass with a low consumption of water.

Abstract: Exemplary embodiments provided herein include genetically engineering microorganisms, such as yeast or bacteria, to produce cannabinoids by inserting genes that produce the appropriate enzymes for the metabolic production of a desired compound.

Abstract: An acidic substance having a carboxyl group is produced by culturing in a medium a microorganism which has been modified to enhance expression of the ybjL gene, and collecting the acidic substance having a carboxyl group from the medium.

Abstract: Systems and methods for cooling and processing materials are disclosed.

Abstract: An acetyl-CoA-producing microorganism, which is capable of efficiently synthesizing acetyl-CoA using carbon dioxide, and a substance production method using the same are provided. An acetyl-CoA-producing microorganism including an acetyl-CoA production cycle obtained by imparting at least one type of enzymatic activity selected from the group consisting of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, to a microorganism.

Abstract: The present invention relates to methods of modulating the mannose content of recombinant proteins.

Abstract: The present invention relates to methods and systems for scanning, detecting, and monitoring microorganisms on solid or semi-solid media using intrinsic fluorescence (IF) measurements. The methods are further directed to detection, characterization and/or identification of microorganisms on a solid or semi-solid media using intrinsic fluorescence (IF) measurements that are characteristic of said microorganisms.

Abstract: The subject invention pertains to a microfluidic apparatus and methods for screening and isolating a target cell from a population of cells. The apparatus comprises a first microfluidic layer comprising microfluidic channels; a second microfluidic layer comprising microfluidic channels; and a microfluidic cell analysis layer comprising a top hanging blocking structure located directly below each location where the first layer microfluidic channels overlap with the second layer microfluidic channels and a cell trap juxtaposed to each of the top hanging blocking structures. The top hanging blocking structures can close or open the juxtaposed cell trap when either or both the first or second layer microfluidic channels located directly above the top hanging blocking structure are sufficiently pressurized and/or sufficiently depressurized.

Abstract: The present invention provides methods for assessing efficacy of a methotrexate (MTX) dosing regimen in a patient.

Abstract: A method for measuring expression of autoregulatory molecules within living cells is provided. An autoregulatory molecule and marker construct is expressed in vivo, where the marker is cleaved from the construct during translation. The method comprises the expression of a construct having an autoregulatory molecule bound to a measurable expression marker by a cleavable linker. The cleavable linker is the substrate of a protease, which acts on its substrate in vivo during translation. Cleavage during translation, allows the autoregulatory molecule to fold normally as it would in its native form. The measurable marker is released and available for detection upon cleavage by the protease. As a result, the concentration of the measurable marker is directly related to the level of expression of the autoregulatory molecule.

Abstract: The present disclosure provides methods, devices, systems and compositions for detecting nucleic acids in polymerase chain reaction assays, such as droplet digital polymerase chain reaction (ddPCR) assays. The present disclosure provides methods, devices, systems and compositions for detecting nucleic acids in ddPCR assays using intercalating dyes. A dual surfactant system with at least one fluorosurfactant and at least one non-ionic non-fluorosurfactant may be employed for droplet generation and nucleic acid detection.

Abstract: This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.

Abstract: Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5? end tag and 3? end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence.

Abstract: Methods compositions and kits are provided for performing a chromatin or chromosome conformation capture assay in partitions.

Abstract: Apparatus and method for detecting analyte in a reaction mixture comprising an internal control. The invention is illustrated using amplification and detection of nucleic acids, where the amplification reaction comprises an exogenous internal control. Magnitude of the detection signal serves as the variable for identifying invalid trials, identifying valid trials that are negative for analyte, and identifying trials that are positive for analyte. Detection of a signal indicating probe hybridization can be used for assigning the presence or absence of analyte nucleic acid in validated reactions using only a single detectable label, and without distinguishing the proportion of signal contributed by internal control probe binding, and analyte probe binding.

Abstract: The invention provides monoferrocenyl compounds of general formula (I). The invention also provides substrates labelled with the compounds, functionalised derivatives of the compounds and methods of using the compounds, functionalised derivatives and labelled substrates in electrochemical assays.

Abstract: The method for analyzing biomolecules, includes the steps of: immobilizing biomolecules to be analyzed on surfaces of magnetic microparticles; reacting labeled probe molecules with the biomolecules to be analyzed; collecting and immobilizing the microparticles on a support substrate; and measuring a label on the support substrate. Since single-molecule immobilized magnetic microparticles are used in the present invention, the number of biomolecules can be counted, and since hybridization and an antigen-antibody reaction are performed with the microparticles having biomolecules immobilized thereon dispersed, the reaction can be rapidly performed. Further, the type and the abundance of biomolecules of interest can be determined at a single molecular level, so as to evaluate, in particular, the absolute concentration of biomolecules.

Abstract: Methods of identifying, diagnosing, and prognosing rheumatoid arthritis are provided, as well as methods of treating rheumatoid arthritis. Also provided are methods for identifying effective rheumatoid arthritis therapeutic agents and predicting responsiveness to rheumatoid arthritis therapeutic agents.

Abstract: The disclosure provides methods and systems for nucleic acid amplification including isothermal nucleic acid amplification.

Abstract: Nucleic acids sequences that can be used for nucleic acid amplification, for example quantitative nucleic acid amplification, are provided herein.

Abstract: A non-contact system for sorting monodisperse water-in-oil emulsion droplets in a microfluidic device based on the droplet's contents and their interaction with an applied electromagnetic field or by identification and sorting.

Abstract: A method for determining whether a lysate contains sufficient biological sample material for a nucleic acid amplification reaction that includes preparing the lysate in the presence of at least one compound that inhibits the amplification reaction if insufficient biological sample material was present during preparation of the lysate, but does not inhibit the amplification reaction if sufficient biological sample material was present during preparation of the lysate, subjecting the lysate to the amplification reaction, and analyzing a result of the amplification reaction. Due to the presence of the compound in the amplification reaction, no amplification signal is obtained if insufficient biological sample material was present during preparation of the lysate but an amplification signal is obtained if sufficient biological sample material was present during preparation of the lysate.

Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.

Abstract: The testing for the Lyme disease pathogen, (Borrelia bergdorferi (Bb) and all other Lyme Borrelia), is notoriously difficult. Bb is not by nature a blood loving bacteria, and prefers the climate of avascular tissues such as cartilage. The Borrelia Provocation Procedure disclosed herein proposes to uniquely lure the Lyme Borrelia spirochetes into the blood through a simple procedure of sub-dermal injection of benign tick saliva and co-factors. Lyme Borrelia can then be tested accurately after the provocation injection (BPP), utilizing any Lyme Borrelia detection test ideally as a specific PCR (polymerase chain reaction) test for the most accurate results as there will be abundantly available DNA present in the blood if there is an existing infection. Treatment is more effective after provocation as well, due to the same action of the Bb. The provocation protocol taught herein makes accurate, non-invasive, active direct Lyme infection testing possible, and creates a platform for an effective treatment as well.

Abstract: Unbiased, genomewide and highly sensitive methods for detecting mutations, e.g., off-target mutations, induced by engineered nucleases.

Abstract: Described herein are improved methods, compositions and kits for next generation sequencing (NGS). The methods, compositions and kits described herein enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (which can comprise regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information can be obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein can be useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Abstract: An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed.

Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.

Abstract: The present invention relates to methods to detect an amount of DNA that originates from cells of a given type, where the sample comprising such DNA in admixture with DNA that does not originate from such cells. Such methods are based on differential methylation, at certain regions, of the DNA that originates from the given type of cells compared to the admixed DNA. Such methods have particular application in the detection, from a biological fluid from a pregnant female, of cell free DNA that originates from a foetus or the placenta of a foetus, or the detection, from a biological fluid from an individual, of cell free DNA that originates from cells of a tumor.

Abstract: The present invention relates to methods to detect an amount of DNA that originates from cells of a given type, where the sample comprising such DNA in admixture with DNA that does not originate from such cells. Such methods are based on differential methylation, at certain regions, of the DNA that originates from the given type of cells compared to the admixed DNA. Such methods have particular application in the detection, from a biological fluid from a pregnant female, of cell free DNA that originates from a foetus or the placenta of a foetus, or the detection, from a biological fluid from an individual, of cell free DNA that originates from cells of a tumor.