Abstract: Provided are a recombinant polynucleotide encoding a polypeptide including a reporter moiety, a substrate moiety, and a destabilization moiety, a host cell including the same, and use thereof to measure the level of a protease by using the recombinant polynucleotide.

Abstract: This invention relates to a pharmaceutical composition having thrombolytic activity comprising ADAMTS13, and to methods for treating or preventing a disorder associated with the formation and/or the presence of one or more thrombus and to methods of disintegrating one or more thrombus in a patient in need thereof. Furthermore, the invention relates to the use of a pharmaceutically effective amount of ADAMTS13 for the preparation of a pharmaceutical composition for treating or preventing a disorder associated with the formation or the presence of one or more thrombus and for disintegrating one or more thrombus in a patient in need thereof.

Abstract: There is provided a dried L-glutamate oxidase composition containing an L-glutamate oxidase, which is stable even if it is stored for such a long term as one year or longer. The composition is a dried composition, preferably lyophilized product, containing an L-glutamate oxidase and a disaccharide. A preferred example of the disaccharide is lactose. Content of the disaccharide per 100 U of the L-glutamate oxidase is preferably 0.5 to 50 mg.

Abstract: An apparatus and method for magnetic separation are provided. The apparatus and method can be used to separate magnetically linked targets from unlinked targets in a suspension. The apparatus has a two-dimensional magnetic array that includes a plurality of one-dimensional magnetic arrays that each define a Halbach array. The one-dimensional arrays are positioned adjacent to one another, and the magnetic fields defined by the plurality of one-dimensional arrays are oriented in the same direction across the array surface. A housing can support the plurality of magnetic elements of the two-dimensional magnetic array. The housing defines a container receiving surface on which a container is receivable adjacent the surface of the magnetic array. A container with a plurality of magnetically linked targets and unlinked targets may be positioned in proximity to the array surface to separate the magnetically linked targets from unlinked targets in the suspension.

Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing.

Abstract: Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery.

Abstract: A method of screening is provided including providing a combination of a plurality of proliferating cell types wherein each proliferating cell type has a unique associated barcode within its genome that is different from other proliferating cell types of the plurality and wherein each proliferating cell type includes an exogenous gene that when expressed produces an associated phenotype to the proliferating cell type which alters proliferation of the cell type, introducing a perturbation to one or more of the plurality of proliferating cell types, inducing expression of one or more of the exogenous genes, determining the relative number of unique associated barcodes after a period of proliferation, and comparing the relative number of unique associated barcodes to a control relative number of unique associated barcodes to indicate the effect of the perturbation on the one or more of the plurality of proliferating cell types.

Abstract: Provided herein are methods of enriching mutated cell free nucleic acids for detection and diagnosis of cancer. Also provided are methods using a CRISPR-Cas system to target and deplete unwanted more abundant cell free nucleic acid sequences thereby enriching for less abundant sequences.

Abstract: Provided herein is a programmable RNA-activated DNA endonuclease activity associated with a Cmr complex. In one embodiment, the enzyme is a general double-stranded DNA endonuclease. Also provided is a programmable RNA endonuclease activity associated with a Cmr complex. In one embodiment, a Cmr2 protein present in a Cmr complex includes a mutation that reduces RNA-activated DNAse activity of the Cmr complex. In one embodiment, a Cmr4 protein present in a Cmr complex includes a mutation that reduces the RNase activity of the Cmr complex. Compositions including components of a Cmr complex and a CRIS-PR-RNA, and an optional activating RNA, are provided. Also provided are methods for using the compositions, and genetically engineered cells that include components of a Cmr complex and a CRISPR-RNA, and an optional activating RNA.

Abstract: A single stranded nucleic acid biosensor for 2?, 3?-cGAMP is provided. The single stranded nucleic acid may include a 2?, 3?-cGAMP-binding riboswitch domain comprising a transducer stem and a dye-binding aptamer domain that is operably connected to the transducer stem. A 2?, 3?-cGAMP-binding riboswitch domain. The dye-binding aptamer domain can be a Spinach2 aptamer. The 2?, 3?-cGAMP biosensor may further include a signaling chromophore specifically bound to the Spinach2 aptamer domain, where the sensor is configured to fluorescently activate the signaling chromophore upon specific binding of 2?, 3?-cGAMP to the 2?, 3?-cGAMP-binding riboswitch domain. Also provided are methods in which the subject 2?, 3?-cGAMP biosensors find use including methods for determining the level of cGAS activity in a sample or a cell. Nucleic acid constructs and host cells including the same are also provided.

Abstract: The application discloses methods and compositions for the inhibition of the alternative complement pathway. The methods and compositions involve the use of aptamers for inhibiting complement Factor D. The application further provides anti-Factor D aptamers for the treatment of dry age-related macular degeneration, geographic atrophy, wet age-related macular degeneration or Stargardt disease.

Abstract: The invention relates to aptamers which specifically bind to immunoglobulin G and their use in the purification of said protein.

Abstract: The present invention relates to RNAi constructs with minimal double-stranded regions, and their use in gene silencing. RNAi constructs associated with the invention include a double stranded region of 8-14 nucleotides and a variety of chemical modifications, and are highly effective in gene silencing. The RNAi constructs may be, for instance, miRNA constructs that are miRNA modulators.

Abstract: Provided are compositions and methods for enhancing recombinant protein production. The compositions and methods involve use of Ribose Binding Protein (RBP) as a segment of a fusion polypeptide, whereby the RBP segment enhances production of the fusion protein. The fusion proteins contain the RBP sequentially in a single fusion protein with a polypeptide for which enhanced expression is desired. Recombinant expression vectors encoding the fusion proteins that contain and RBP segment are included, as are cells that contain the expression vectors. Methods for separating fusion proteins and for liberating a polypeptide segment that is part of the fusion protein are also provided.

Abstract: Compositions and methods for production of monoclonal antibodies are provided according to aspects of the present invention including a synthetic gene circuit system, comprising: a first expression construct comprising a nucleic acid encoding tetracycline transactivator (tTA) operably linked to a ubiquitous promoter; a second expression construct comprising a nucleic acid encoding tetracycline transactivator (tTA) operably linked to a tetracycline responsive element (TRE); a third expression construct comprising a nucleic acid encoding a heavy chain component of an monoclonal antibody operably linked to a TRE; and a fourth expression construct comprising a nucleic acid encoding a light chain component of an monoclonal antibody operably linked to a TRE, functioning of the system includes a positive feedback loop which amplifies expression of the heavy chain component of the monoclonal antibody and the light chain component of the monoclonal antibody.

Abstract: The present invention relates to hybrid nucleic acid sequence constructs comprising a CRISPR nucleic acid sequence and a DNA repair template associated with each other in a covalent and/or non-covalent way for CRISPR based genome engineering. Further provided is a molecular complex additionally comprising at least one CRISPR polypeptide. All components within the complex are in physical proximity. In addition, there is provided a plant, plant cell, a plant material, or a derivative, or progeny thereof comprising the hybrid RNA/DNA sequence and/or the molecular complex. Further, there is provided a method for modifying at least one DNA target sequence in a prokaryotic or eukaryotic cell as well as a method for manufacturing a plant or plant cell. Finally, there is provided the use of at least one hybrid RNA/DNA sequence, or use of a molecular complex for gene editing or genome engineering in a prokaryotic or eukaryotic cell or organism.

Abstract: This disclosure concerns compositions and methods for promoting transcription of a nucleotide sequence in a plant or plant cell, employing a Zea mays GRMZM2G144030 promoter. Some embodiments relate to a Zea mays GRMZM2G144030 promoter that functions in plants to promote transcription of operably linked nucleotide sequences. Other embodiments relate to a Zea mays GRMZM2G144030 3?UTR that functions in plants to terminate transcription of operably linked nucleotide sequences.

Abstract: This disclosure concerns compositions and methods for promoting transcription of a nucleotide sequence in a plant or plant cell, employing a promoter from a Zea mays KN1 gene. Some embodiments relate to a promoter from a Zea mays KN1 gene that functions in plants to promote transcription of operably linked nucleotide sequences.

Abstract: The inventive technology relates to systems and methods for enhanced in vivo production, accumulation and modification of cannabinoids. In one embodiment, the invention may include systems and methods for enhanced in vivo biosynthesis of chemically-modified water-soluble cannabinoids in a whole plant, or a cell suspension culture system.

Abstract: This disclosure relates to the isolation and sequencing of nucleic acid molecules that encode cytochrome P450 polypeptides from a Papaver somniferum cultivar; uses in the production of noscapine and identification of poppy cultivars that include genes that comprise said nucleic acid molecules.

Abstract: The present disclosure provides a transgenic plant comprising one or more nucleotide sequences encoding polypeptides selected from photosystem II subunit S (PsbS), zeaxanthin epoxidase (ZEP), and violaxanthin de-epoxidase (VDE), operably linked to at least one expression control sequence. Expression vectors for making transgenic plants, and methods for increasing biomass production and/or carbon fixation and/or growth in a plant comprising increasing expression of at least one of PsbS, ZEP and VDE polypeptides are also provided.

Abstract: Methods for producing plants with improved tolerance to stresses, such as drought or salinity, and transgenic plants made by the methods are disclosed. The methods comprise overexpressing a wax synthase/acyl-CoA:diacylglycerol acyltransferase (WSD1) in the plant.

Abstract: Isolated polynucleotides having a nucleic acid sequence at least 80% homologous to SEQ ID NO:1, 3, 5, 7, 9, 11, 158, 159, 160, 161, 162-204, 206-211, 214-287 and/or encoding polypeptides having an amino acid sequence at least 80% homologous to SEQ ID NO: 2, 4, 6, 8, 10, 12, 13-56, 58-63, 66-121, 141-156 or 157 are provided. Also provided are methods of utilizing same for increasing the tolerance of a plant to abiotic stresses and/or increasing the biomass, vigor and/or yield of a plant.

Abstract: The invention provides recombinant DNA molecules and constructs, as well as their nucleotide sequences, useful for modulating gene expression in plants. The invention also provides transgenic plants, plant cells, plant parts, and seeds comprising the recombinant DNA molecules operably linked to heterologous transcribable DNA molecules, as are methods of their use.

Abstract: OsACBP5 can be used to enhance tolerance to fungal necrotrophs in genetically modified plants. OsACBP5-overexpressing transgenic Arabidopsis were conferred enhanced tolerance to fungal necrotrophs such as root-infecting necrotroph Rhizoctonia solani and shoot-infecting necrotrophs (Botrytis cinerea and Alternaria brassicicola). Vectors/expression cassettes for conferring tolerance to fungal necrotrophs to plants/plant material are provided. Methods of using OsACBP5 to enhance tolerance to fungal necrotrophs are provided. Plants and plant material with improved tolerance to fungal necrotrophs are also provided. Methods for screening for genes with OsACBP5-like activity are also provided.

Abstract: This disclosure concerns nucleic acid molecules and methods of use thereof for control of insect pests through RNA interference-mediated inhibition of target coding and transcribed non-coding sequences in insect pests, including coleopteran pests. The disclosure also concerns methods for making transgenic plants that express nucleic acid molecules useful for the control of insect pests, and the plant cells and plants obtained thereby.

Abstract: The present invention relates to the identification of a new class of fatty acid decarboxylases and its uses, in particular for producing alkanes/alkenes from fatty acids.

Abstract: The present disclosure is directed, in a first aspect, to the use of inverting beta-xylosidase enzymes to reduce byproduct formation and increase the yield of fermentation products, as well as, in a second aspect, to the use of retaining beta-xylosidase enzymes to improve production of alkyl-beta-xylopyranoside compounds, in a simultaneous saccharification and fermentation reactions.

Abstract: A process for the creation of ethanol from cellulosic materials using the bacteria Cellulomonas sp. and aerobic Zymomonas mobilis in the same medium under the same conditions to breakdown cellulosic materials into glucose and to ferment that glucose into ethanol and three significant byproducts, glycerol, acetic acid, and lactic acid.

Abstract: Biomass feedstocks (e.g., plant biomass, animal biomass, and municipal waste biomass) are processed to produce useful products, such as fuels. For example, systems are described that can convert feedstock materials to a sugar solution, which can then be fermented to produce ethanol. Biomass feedstock is saccharified in a vessel by operation of a jet mixer, the vessel also containing a liquid medium and a saccharifying agent.

Abstract: Methods and systems for the production of alcohols are described. A two stage process is utilized, where fermentation in a first stage produces an intermediate product, such as an amino acid or organic acid, from a carbon containing feedstock. A second stage produces alcohol by fermentation of this intermediate product.

Abstract: A method for producing an objective substance such as vanillin and vanillic acid is provided. An objective substance is produced from a carbon source or a precursor of the objective substance by using a microorganism that is able to produce the objective substance, which microorganism has been modified so that the activity of an enzyme involved in SAM cycle (SAM cycle enzyme) is increased.

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 concerns an oleaginous yeast variant of the species Rhodosporidium azoricum characterized by higher biomass yields and intra-cellular lipid accumulation useful for the production of bio-fuels higher, in determined conditions, with respect to the wild type strain of the same species. Furthermore, the invention concerns a method through which said oleaginous yeast variant of the species Rhodosporidium azoricum was obtained. The invention further concerns the lipid production by means of said variant strain of oleaginous yeast of the species Rhodosporidium azoricum.

Abstract: The present invention discloses a single-cell factory for efficiently synthesizing ?-aminobutyric acid and construction and application thereof, which belong to the technical field of microorganisms. The present invention expresses an L-threonine deaminase gene, an L-amino acid dehydrogenase gene and a dehydrogenase gene for providing cofactor NADH cycle in tandem to construct a recombinant Escherichia coli single-cell factory which is used for efficiently synthesizing ?-aminobutyric acid. The expression level of the L-threonine deaminase is optimized and controlled by an RBS sequence, so that the problem of transformation inhibition caused by the rapid accumulation of an intermediate product ketobutyric acid is solved, moreover, the expression level of the dehydrogenase for providing cofactor NADH cycle is optimized and controlled by a promoter and an RBS sequence, consequently, the NADH regeneration rate is increased, and ultimately, yield is increased.

Abstract: A method for producing an L-amino acid such as L-lysine is provided. An L-amino acid is produced by culturing a bacterium having an L-amino acid-producing ability, which has been modified so that the activity of a carotenoid biosynthesis enzyme is increased, in a medium, and collecting the L-amino acid from the medium.

Abstract: The present disclosure describes methods and systems for improving the expression of a properly folded, biologically active protein of interest in a cell free synthesis system. The methods and systems use a bacterial cell free extract having an active oxidative phosphorylation system, and include an exogenous protein chaperone. The exogenous protein chaperone can be expressed by the bacteria used to prepare the cell free extract. The exogenous protein chaperone can be a protein disulfide isomerase and/or a peptidyl-prolyl cis-trans isomerase. The inventors discovered that the combination of a protein disulfide isomerase and a peptidyl-prolyl cis-trans isomerase produces a synergistic increase in the amount of properly folded, biologically active protein of interest.

Abstract: Melanin or inorganic fertilizers are produced from fermentation leachates or from low-cost nutrient-rich solutions. The method for producing the melanin or inorganic fertilizer comprises repetitive trophic cycling in the controlled conditions of primary and secondary bioreactors. Nutrients are cycled between microorganisms such as bacteria, yeast and fungi and black soldier fly larvae, Hermetia illucens. Polysaccharides are partly converted into natural melanins or inorganic fertilizer, which are difficult to biodegrade and hence accumulate in the bioreactors. The method can employ, as a source of nutrients, leachates produced from food waste or from sugar-rich liquid waste of the food industry. These leachates can be used raw or can be augmented with low-cost sugar-rich solutions such as molasses, hydrolyzed cellulose or starch. The method is inexpensive and does not require the use of expensive chemically-defined culture media.

Abstract: The present invention relates to a method of producing activated clostridial neurotoxins that are essentially free of unactivated products, to compositions comprising such and to their use in therapy.

Abstract: Computer-implemented processes for precision therapeutic biomarker screening for cancer include using a model-based overlapping clustering framework to assess large numbers of possible drugs and drug combinations against patient data, including cell line responsiveness. A multivariate regression model has been developed, along with a latent overlapping cluster indicator variable. The techniques employ a new finite mixture of multivariate regression (FMMR) model and expectation-maximization (EM) algorithm for modeling. The techniques can analyze large amounts of drug data and identify complex overlapping drug clusters, as well as cluster-wise drivers that facilitate identification of new drugs for treating pathologies, such as cancer, in patients.

Abstract: Method for testing a sample of body fluid for the presence of bacteria and comprising the steps of adjusting the dilution of the sample to a predetermined concentration, of dividing the diluted sample into two batches defining a baseline-batch and a control-batch, of testing the baseline-batch at a time T0 with the flow cytometer to obtain enumerative baseline bacterial values, of culturing the control-batch in growth media between times T0 and T1, of testing the control-batch at time T1 with the flow cytometer to obtain enumerative control bacterial values, and of comparing the control values to the baseline values to determine a bacteria growth-ratio.

Abstract: Provided herein are systems and components thereof for improving protease activity. The systems make use of an emulsion for in vitro compartmentalization of a library of synthetic compounds, each compound having a gene linked to a protease substrate and selectable marker. Expressed enzymes with greater protease activity will preferentially hydrolyze the protease substrate, whereas enzymes with less protease activity will leave the substrate intact. Removal of the non-hydrolyzed compounds provides an enriched gene library encoding for more active protease variants. Also described are synthetic compounds and emulsions which can be used in the methods.

Abstract: Provided are methods for the identification of mutant kinases that are resistant to inhibition by a kinase inhibitor. In some embodiments, the methods may be used to assess a test compound or kinase inhibitor for the risk of the development of resistance in vivo, e.g., during clinical administration to treat a disease such as a cancer.

Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.

Abstract: Provided is a method of modifying a target site in the genome of a eukaryotic cell, the method comprising: (1) a step of introducing into the cell, introduction nucleic acids comprising (a) a template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease, (b) a template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or a guide RNA, and (c) a template nucleic acid comprising a nucleic acid sequence encoding a selectable marker; and (2) a step of selecting a cell expressing the selectable marker, wherein the number of moles (C) of (c) the template nucleic acid comprising a nucleic acid sequence encoding a selectable marker, subjected to the step (1), is smaller than any of the number of moles (A) of (a) the template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease and the number of moles (B) of (b) the template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or the guide RNA.

Abstract: The invention relates to the use of inductively coupled plasma mass spectroscopy for cellular sample analysis. In some embodiments a method of performing mass spectroscopy analysis using an inductively coupled plasma mass spectroscopy system is provided. The method may include introducing a cellular sample comprising one or more cells or cellular particles into an inductively coupled plasma of the inductively coupled plasma mass spectroscopy system. The method may further include using the inductively coupled plasma mass spectroscopy system to assess the cellular sample by detecting and measuring one or more element tags in the cellular sample based on the element or isotopic compositions of the one or more element tags.

Abstract: In the case of using a blocking nucleic acid to prevent non-specific hybridization of a target nucleic acid with a nucleic acid probe, further excellent efficiency of detecting the target nucleic acid is achieved. A buffer composition used in hybridization of a target nucleic acid with a nucleic acid probe, wherein the buffer composition for hybridization contains a blocking nucleic acid comprising a nucleotide sequence complementary to a region comprising at least a non-detection target nucleotide in a non-target nucleic acid, in a concentration of one or more times higher than the concentration of a nucleic acid in a nucleic acid mixture consisting of the target nucleic acid and the non-target nucleic acid.

Abstract: The present disclosure provides the quantification of double-strand breaks in DNA molecules using terminal deoxynucleotidyl transferase using a preliminary step of nick gap and repair. This preliminary step comprising contacting the DNA molecules with both a DNA ligase and a DNA polymerase to repair DNA nicks and remove DNA gaps prior to using the terminal deoxynucleotidyl transferase.

Abstract: Methods of detecting or quantifying short RNA or DNA molecules using split cycle amplification are provided.

Abstract: Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.