Abstract: The present disclosure methods for identifying binding partners using cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of peptides that bind to targets of interest. The engineered peptides are preferably expressed in the cells under conditions that provide both secretion and display of the engineered peptides on the cell surfaces, thus providing access of the engineered peptides to identify potential binding pairs. The cell libraries cab be engineered using an automated editing system that provides for one or more targeted edits per cell.

Abstract: There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.

Abstract: Provided herein is a pathway for adipocyte energy consumption regulation involving ARID5B, genetic variant rs1421085, IRX3, and IRX5. Compositions and methods for modulating the pathway in vitro and in vivo for anti-cachectic and anti-obesity effects are provided. Methods of identifying subjects at risk of developing a disorder mediated by a dysregulation of the energy consumption pathway are also provided.

Abstract: This disclosure relates to novel huntingtin targets. Novel oligonucleotides for the treatment of Huntington's disease are also provided.

Abstract: The present invention includes a composition and method for the treatment of an eye disease comprising a therapeutically effective amount of an autophagy stimulator that treats or slows the progression of the eye disease by enhancing or stimulating autophagy or correcting an autophagy deficiency.

Abstract: The inventive technology relates to novel paratransgenic strategies for the biocontrol of pathogens in animal systems using interfering RNA molecules expressed in genetically modified bacteria that may be configured to colonize a target host. In one preferred embodiment, the invention includes novel paratransgenic strategies for the biocontrol of pathogens in aquatic organisms raised in aquaculture environments.

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.

Abstract: The present invention provides a method of inducing insulin production in a cell by up-regulating a target gene involved in insulin production in said cell using an saRNA (short activating ribonucleic acid) which specifically targets a target antisense RNA transcript present in said cell.

Abstract: The present invention is related to a ribonucleic acid comprising a double stranded structure whereby the double-stranded structure comprises a first strand and a second strand, whereby the first strand comprises a first stretch of contiguous nucleotides and whereby said first stretch is at least partially complementary to a target nucleic acid, and the second grand comprises a second stretch of contiguous nucleotides whereby said second stretch is at least partially identical to a target nucleic acid, and whereby the double stranded structure is blunt ended.

Abstract: The present embodiments provide methods, compounds, and compositions useful for inhibiting PNPLA3 expression, which may be useful for treating, preventing, or ameliorating a disease associated with PNPLA3.

Abstract: The invention relates to compositions and methods for making and using recombinant bacteria that are capable of regulated attenuation and/or regulated expression of one or more antigens of interest.

Abstract: There are provided compositions and methods for transforming plants, preferably monocot, and even more preferably, sugarcane. The transformation methods involve infection of plant tissue with Agrobacterium, and co-cultivation using culture medium comprising high concentrations of gelling agent, with the result of inhibiting the exacerbated growth of the bacteria and increasing the transformation frequencies. The invention includes regenerating transformed plants, and the transformed plants themselves.

Abstract: This disclosure concerns synthetic polynucleotides encoding a polypeptide of interest that are particularly well-suited for expression in target plants.

Abstract: The present invention is directed to a soybean plant with mutations in FAD2-1A and FAD2-1B. Moreover, the present invention is directed to seeds from said plants with altered ratios of monosaturated and polyunsaturated fats. In particular, the present invention is directed to plants where the plants exhibit elevated levels of oleic acid.

Abstract: The present invention provides methods and compositions for targeting enzymes involved in lignin or xylan biosynthesis using genome editing nucleases to specifically reduce content in a desired plant cell type(s).

Abstract: Isolated polynucleotides are provided. Each of the isolated polynucleotides comprise a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 80% homologous to SEQ ID NO: 121, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 125, 126, 95 or 96, wherein the polypeptide is capable of regulating cotton fiber development. Also provided are methods of using such polynucleotides for improving fiber quality and/or yield of a fiber producing plant, as well as methods of using such polynucleotides for producing plants having increased biomass/vigor/yield.

Abstract: Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NOs: 710-1153 and 9276-15726, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-709 and 1157-9275, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

Abstract: The invention provides cotton event MON 88701, and plants, plant cells, seeds, plant parts, and commodity products comprising event MON 88701. The invention also provides polynucleotides specific for event MON 88701 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event MON 88701. The invention also provides methods related to event MON 88701.

Abstract: The invention pertains to a plant cell or a plant having one or more mutations in the promoters of both the alleles for CsLOB1 gene, wherein the one or more mutations are in the promoter binding sites for PthA4 protein from Xanthomonas spp., and wherein the one or more mutations reduce or abolish the binding of the Xanthomonas spp. PthA4 protein on to the binding sites in the promoters of the CsLOB1 genes. Also, a plant cell or a plant having one or more mutations in the coding regions of both the alleles for CsLOB1 gene, wherein the one or more mutations reduce or abolish the binding of the function of CsLOB1 protein are provided. The invention further pertains to the methods of making the plant cell or the plant resistant to infection by Xanthomonas spp.

Abstract: Vector compositions comprising a myeloproliferative sarcoma virus enhancer, negative control region deleted, dl587rev primer-binding site substituted (MND) promoter operably linked to a chimeric antigen receptor (CAR) are provided.

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: The invention features methods for producing isoprene from cultured cells wherein the cells in the stationary phase. The invention also provides compositions that include these cultured cells and/or increased amount of isoprene. The invention also provides for systems that include a non-flammable concentration of isoprene in the gas phase. Additionally, the invention provides isoprene compositions, such as compositions with increased amount of isoprene or increased purity.

Abstract: The invention relates to methods and bacterial strains for making terpene and terpenoid products, the bacterial strains having improved carbon pull through the MEP pathway and to a downstream recombinant synthesis pathway.

Abstract: The present application relates to recombinant microorganisms useful in the biosynthesis of monoethylene glycol (MEG) and one or more three-carbon compounds such as acetone, isopropanol or propene. The MEG and one or more three-carbon compounds described herein are useful as starting material for production of other compounds or as end products for industrial and household use. The application further relates to recombinant microorganisms co-expressing a C2 branch pathway and a C3 branch pathway for the production of MEG and one or more three-carbon compounds. Also provided are methods of producing MEG and one or more three-carbon compounds using the recombinant microorganisms, as well as compositions comprising the recombinant microorganisms and/or optionally the products MEG and one or more three-carbon compounds.

Abstract: The present application relates to recombinant microorganisms useful in the biosynthesis of monoethylene glycol (MEG) and one or more three-carbon compounds such as acetone, isopropanol or propene. The MEG and one or more three-carbon compounds described herein are useful as starting material for production of other compounds or as end products for industrial and household use. The application further relates to recombinant microorganisms co-expressing a C2 branch pathway and a C3 branch pathway for the production of MEG and one or more three-carbon compounds. Also provided are methods of producing MEG and one or more three-carbon compounds using the recombinant microorganisms, as well as compositions comprising the recombinant microorganisms and/or optionally the products MEG and one or more three-carbon compounds.

Abstract: The present disclosure describes an engineered microorganism for producing alpha omega bifunctional C6-16 fatty acids from renewable carbon sources.

Abstract: The present application relates to a method for fermentative production of oxidized coenzyme Q10 and high-content oxidized coenzyme Q10 prepared therefrom. For the method for fermentative production of oxidized coenzyme Q10, in a fermentation process of a production strain, the oxidation-reduction potential (ORP) of a fermentation broth is controlled to be ?50 to 300 Mv, and preferably the oxidation-reduction potential (ORP) of the fermentation broth is controlled to be 50 to 200 mV. By controlling the ORP of the fermentation broth, the method for fermentative production of oxidized coenzyme Q10 enables the oxidized coenzyme Q10 content in the coenzyme Q10 produced by microorganisms to reach 96% or more, and the product is substantially composed of a single component, which makes post-treatment more convenient.

Abstract: The present invention relates to a method of preparing an anthocyanin oligomer using a coenzyme derived from an Aspergillus sp. strain, and more particularly to a method of preparing an anthocyanin oligomer by fermenting an anthocyanin monomer with a coenzyme of Aspergillus niger, which is a kind of Aspergillus sp. strain. According to the present invention, in order to overcome contamination problems during the culturing process using Aspergillus niger, a coenzyme of Aspergillus niger is extracted and the fermentation process is performed using the same, whereby an anthocyanin oligomer characterized by reduced concern of contamination and superior radical-scavenging effects, compared to existing anthocyanin monomers, can be produced.

Abstract: A method for producing insoluble alpha-1,3-glucan is disclosed. Embodiments of the method comprise providing (i) oligosaccharides that comprise alpha-1,3 and alpha-1,6 glycosidic linkages, or (ii) oligosaccharides derived from a glucosyltransferase reaction; and contacting at least water, sucrose, a glucosyltransferase enzyme, and the oligosaccharides provided in the first step. Glucosyltransferase reaction compositions embodying such a method, and insoluble products thereof, are also disclosed. Yield and other product benefits can be realized when practicing the disclosed subject matter.

Abstract: Disclosed herein are methods of manufacturing therapeutic proteins.

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: The present invention relates to a genetically-engineered Mycobacterium strain and a use thereof in the preparation of steroidal compounds. The genetically-engineered Mycobacterium strain is a Mycobacteria which lacks of acyl-CoA dehydrogenase genes fadE31, fadE32 and fadE33, wherein acyl-CoA dehydrogenase genes fadE31, fadE32 and fadE33 respectively encode proteins as follows: having amino acid sequences according to SEQ ID NOs 4, 6 and 8; derived by substituting, deleting or inserting one or more amino acids in the amino acid sequence defined by preceding protein and having the same function as that of the preceding protein. The present invention constructs a genetically-engineered Mycobacterium strain and applies it in preparing steroidal compounds, thereby enriching the types of valuable intermediates, improving the production efficiency and product quality of steroid drugs, reducing energy consumption in the steroid drugs production, simplifying production steps, and reducing production costs.

Abstract: The invention relates to transaminases and their use. The ATAs according to the invention are particularly useful for catalyzing the conversion of amines to ketones and/or vice versa. Preferably, the transaminase (ATA) according to the invention comprises an amino acid sequence with at least 80% homology to SEQ ID NO:1, wherein the amino acid sequence is engineered compared to SEQ ID NO:1 such that it comprises at least a substitution selected from the group consisting of F255L, F255A, F255C, F255D, F255E, F255G, F255H, F255K, F255M, F255N, F255P, F255Q, F255R, F255S, F255T, F255V, F255W, and F255Y.

Abstract: Disclosed herein are methods and systems for determining whether a cell is resistant to one or more drugs. Also, disclosed herein are methods and systems for monitoring the treatment of a cancer patient to determine whether the cancerous cells being treated are resistant to the treatment. Further, disclosed herein are methods and systems for predicting the responsiveness of a cell to a drug. Also, disclosed herein are methods and systems to determine the rate of the efficacy of a chemotherapeutic drug on a cancerous, neoplastic or damaged cells.

Abstract: Methods, kits and reagents are provided for increasing the sensitivity of detecting the presence or absence of endospores by increasing the available protein for detection. The methods are fast and amendable to testing in a non-laboratory setting and use a protein detection reagent and solid microparticles.

Abstract: Herein is provided a simple, reliable and accurate method for cellular analysis on hematology analyzers. In various aspects, the methods provide separation and/or differentiation between red blood cells (RBCs) and white blood cells (WBCs) by utilizing a fluorescent dye to selectively stain WBCs such that they emit stronger fluorescence signals. The method provides optimal detection limits on WBCs and RBCs, thereby allowing analysis of samples with sparse cellular concentrations. As few as one reagent may be used to prepare a single dilution for body fluid analysis, in order to simplify the body fluid analysis. Minimal damage to WBCs is attained using the lysis-free approach described in aspects of the disclosure.

Abstract: Provided herein is a method for determining the number of sites of infection of a cell culture, including the steps of: infecting a cell culture arranged in a sample carrier with viruses, counting any infected areas of the cell culture by means of a transmitted light method, marking infected cells with fluorescence markers, counting infected areas of the cell culture by means of a fluorescence analysis method, and evaluating area by area the areas determined in both methods for determining the number of sites of infection.

Abstract: The invention relates to a method for identifying unknown microbes in a sample, wherein a mass spectrometric determination down to the taxonomic level of the genus or species is supplemented by a detailed determination of a lower taxonomic level or variety by means of infrared spectrometry, using restricted reference libraries of infrared spectra. These libraries can be genus-specific, containing only infrared spectra of microbes of one genus, or species-specific, containing only infrared spectra of microbes of one species. In so doing, a robust mass spectrometric identification of the species of unknown microbes is advantageously supplemented with a detailed analysis of the subspecies and varieties by means of infrared spectrometry, primarily in order to identify medically important varieties such as pathovars like EHEC and EPEC, and antibiotic-resistant microbes like MRSA.

Abstract: Sample preparation unit, preferably for sterility testing: a housing body including at least two ports adapted to serve as fluid inlet and/or fluid outlet, a membrane support, and a lid part such that a membrane chamber is defined adjacent said membrane support. One of at least two ports is arranged so as to allow a fluid transfer to/from a first volume of the membrane chamber at a position upstream of a membrane to be placed on the membrane support, and the other ports arranged to allow fluid transfer to/from a second volume of said membrane chamber at a position downstream of a membrane to be placed on said membrane support. A movable part is provided on housing body such that the movable part and housing body are movable relative to each other, selectively interrupting/establishing fluid transfer between at least one of two ports and the membrane chamber.

Abstract: Methods of detecting a local infection, critical colonization, or infection in a wound, predicting wound healing in a wound, and detecting bacterial pathogenesis in a wound are provided.

Abstract: An isolated polynucleotide encoding a modified luciferase polypeptide and substrates. The OgLuc variant polypeptide has at least 60% amino acid sequence identity to SEQ ID NO: 1 and at least one amino acid substitution at a position corresponding to an amino acid in SEQ ID NO: 1. The OgLuc variant polypeptide has at least one of enhanced luminescence, enhanced signal stability, and enhanced protein stability relative to the corresponding polypeptide of the wild-type Oplophorus luciferase.

Abstract: Provided herein are methods and compositions for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample. The methods and compositions are applicable to biological, clinical, forensic, and environmental samples.

Abstract: A method for making a polynucleotide is provided including (a) delivering one or more reaction reagents including an error prone or template independent DNA polymerase, cations and a selected nucleotide to a reaction site including an initiator sequence having a terminal nucleotide for a time period and under conditions capable of covalently adding one or more of the selected nucleotide to the terminal nucleotide at the 3? end of the initiator such that the selected nucleotide becomes a terminal nucleotide, and (b) determining whether the selected nucleotide has been added to the terminal nucleotide, wherein if the selected nucleotide has not been added to the terminal nucleotide, then repeating step (a) until the selected nucleotide has been added, and (c) repeating steps (a) and (b) until the polynucleotide is formed.

Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include providing nucleic acid containing-cellular samples from blood or FFPE samples, lysing cells of the sample to liberate nucleic acids, and performing tagmentation without purifying the liberated nucleic acids.

Abstract: Disclosed is nucleic acid preserving compositions and methods of manufacturing and using the same. Compositions include a carrier, a chaotropic agent, a buffering agent, a chelating agent, a surfactant, an alcohol, an acid, and a mucolytic agent. Compositions as aqueous solutions can include water as a carrier. Preferred embodiments include water, guanidine thiocyanate, Tris, EDTA, SLS, SDA 3C, HCl, and N-acetyl-L-cysteine. Some embodiments include a colored dye as a visual indicator. Methods of manufacturing include combining the components into a mixture, such as an aqueous solution. Methods of use include providing a biological sample that includes nucleic acid and contacting the biological sample with the composition. Kits include the composition disposed in a portion of a biological sample collection apparatus.

Abstract: The present disclosure provides systems and methods for making a hydrogel comprising a cell, cell nucleus, or one or more components derived from a cell or cell nucleus. A method for making a hydrogel may comprise providing a cell or cell nucleus, a first polymer, wherein the first polymer comprises a plurality of first crosslink precursors, each of the plurality of first crosslink precursors comprising an azide group; providing a second polymer, wherein the second polymer comprises a plurality of second crosslink precursors, each of the plurality of second crosslink precursors comprising an alkyne group; and crosslinking the first polymer and the second polymer via a reaction between a first section of the first crosslink precursors and a second section of the second crosslink precursors, thereby providing the hydrogel comprising the cell or cell nucleus.

Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Abstract: Imaging systems including an objective lens and a line generation module are described herein. The objective lens may focus a first light beam emitted by the line generation module and a second light beam emitted by the line generation module at a focal point external to a sample so as to adjust line width. Line width may be increased to lower overall power density of a light beam on a surface of the sample such that the power density of the light beam on the surface of the sample is below a photosaturation threshold of a dye on the sample.

Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.

Abstract: The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.