Abstract: The present invention relates to an universal antibody acceptor framework and to methods for grafting non-human antibodies, e.g., rabbit antibodies, using a universal antibody acceptor framework. Antibodies generated by the methods of the invention are useful in a variety of diagnostic and therapeutic applications.

Abstract: Provided herein, in some aspects, are tools (e.g., methods, compositions and nucleic acids) for building genetic circuits in Bacteroides and Parabacteroides bacteria, as well as the bacteria containing the genetic circuits.

Abstract: The present invention is directed to methods and compositions for targeted gene silencing that provide the ability to not only repress expression but to modulate the repression of expression of one or more target genes. In one aspect, a recombinant nucleic acid molecule is provided comprising a nucleotide sequence encoding a subset of CRISPR-cas polypeptides, or functional fragments thereof, from a type-I CRISPR-cas system. In some aspects, a recombinant nucleic acid of the invention comprises a nucleotide sequence encoding three or more Type I Cascade polypeptides having substantial identity to a type I Cascade polypeptide.

Abstract: The present invention provides a microorganism-derived soluble coenzyme-binding glucose dehydrogenase which catalyzes a reaction for oxidizing glucose in the presence of an electron acceptor, has an activity to maltose as low as 5% or less, and is inhibited by 1,10-phenanthroline. The invention also provides a method for producing the coenzyme-binding glucose dehydrogenase, and a method and a reagent for measuring employing the coenzyme-binding glucose dehydrogenase. According to the invention, the coenzyme-binding glucose dehydrogenase can be applied to an industrial field, and a use becomes possible also in a material production or analysis including a method for measuring or eliminating glucose in a sample using the coenzyme-binding glucose dehydrogenase as well as a method for producing an organic compound. It became also possible to provide a glucose sensor capable of accurately measuring a blood sugar level.

Abstract: The present invention provides AAV capsid proteins comprising modification of one or a combination of the surface-exposed lysine, serine, threonine and/or tyrosine residues in the VP3 region. Also provided are rAAV virions comprising the AAV capsid proteins of the present invention, as well as nucleic acid molecules and rAAV vectors encoding the AAV capsid proteins of the present invention. Advantageously, the rAAV vectors and virions of the present invention have improved efficiency in transduction of a variety of cells, tissues and organs of interest, when compared to wild-type rAAV vectors and virions.

Abstract: Transgenic silkworms stably expressing synthetic spider silk genes or composite silkworm/spider silk genes are disclosed. The exogenous spider silk genes are stably intergrated into a defined site of the fibroin heavy chain intron or a fibroin light chain intron of silkworms. Synthetic spider silk proteins and composite spider silk-silkworm genes and proteins are provided. The expression of exogenous spider silk genes is driven by the endogenous fibroin heavy chain promoter, improving the genetic stability of transgenic silkworms. The composite silkworm/spider silk fibers exhibit exceptional mechanical performance, compared to normal silkworm silk fibers and other transgenic silkworm fibers.

Abstract: Disclosed are recombinant strain of a genus Corynebacterium capable of producing biliverdin IX-alpha (IX?) and a method of producing biliverdin IX-alpha using the same. The recombinant strain is capable of synthesizing biliverdin IX-alpha in an environmentally friendly manner using only glucose without the addition of any nitrogen source, thus replacing the synthesis of biliverdin IX-alpha through chemical treatment, which is a conventional synthetic method causing environmental pollution problems.

Abstract: A group of molecular biomarkers having the genes SLC35D3, POSTN, KLK6 and MUC2 can be used in objective and quantitative methods for the classification, prediction of prognosis and for guiding treatment decisions of a subject with colorectal cancer. More specifically, a method for determining the metastatic potential and/or tumor aggressiveness of a colorectal cancer in a subject can include determining the gene expression levels of genes SLC35D3, POSTN, KLK6 and/or MUC2 in a regional lymph node, a primary intestinal tumor, blood, or feces sample obtained from the subject.

Abstract: The present invention is intended to provide a highly versatile and simple technique which can increase the expression level of a protein in an E. coli expression system or a yeast expression system. Using an E. coli expression system or a yeast expression system, a target protein is expressed as a tag-added protein to which a peptide tag composed of an amino acid sequence SK, SKX, SKXX (SEQ ID NO. 1), AKXX (SEQ ID NO. 29), or KKXX (SEQ ID NO. 30) (wherein X represents any amino acid residue) is linked at the N-terminal.

Abstract: Disclosed are compositions and methods for expressing and purifying a peptide of interest using a Flagellar Type III secretion system. Disclosed are nucleic acid sequences that contain a FlgM nucleic acid sequence, a cleavage site, and a nucleic acid sequence of interest. Also disclosed are polypeptides that contain FlgM, a cleavage site and a peptide of interest. Methods of producing polypeptides that have FlgM, a cleavage site and a peptide of interest are provided.

Abstract: The present invention relates to methods for obtaining positive transformants of a filamentous fungal host cell, comprising: transforming a tandem construct into a population of cells of the filamentous fungal host a tandem construct and isolating a transformant of the filamentous fungal host cell comprising the tandem construct. The present invention also relates to such tandem constructs, filamentous fungal host cells comprising such tandem constructs, and methods of producing multiple recombinant proteins.

Abstract: The present invention relates to the field of bacteriology. In particular, the invention relates to methods and compositions for treatment and prevention of infection in wounds, and methods for producing and storing bacterial donor organisms for conjugation-based antibacterial agents. The present invention relates to the field of bacteriology and pharmacology. In particular, the invention relates to novel compositions (e.g., antimicrobial agents) and methods of using the same for treating tissue (e.g., lesions of the skin and other soft tissues) comprising the killing or altering (e.g., inhibiting) growth and virulence of populations of microorganisms.

Abstract: The present invention provides a genetically modified lactic acid bacterium capable of producing diacetyl under aerobic conditions. Additionally the invention provides a method for producing diacetyl using the genetically modified lactic acid bacterium under aerobic conditions in the presence of a source of iron-containing porphyrin and a metal ion selected from Fe3+, Fe2+ and Cu2+. The lactic acid bacterium is genetically modified by deletion of those genes in its genome that encode polypeptides having lactate dehydrogenase (E.C 1.1.1.27/E.C.1.1.1.28); ?-acetolactate decarboxylase (E.C 4.1.1.5); water-forming NADH oxidase (E.C. 1.6.3.4); phosphotransacetylase (E.C.2.3.1.8) activity; and optionally devoid of or deleted for genes encoding polypeptides having diacetyl reductase ((R)-acetoin forming; EC:1.1.1.303); D-acetoin reductase; butanediol dehydrogenase ((R,R)-butane-2,3-diol forming; E.C. 1.1.1.4/1.1.1.-) and alcohol dehydrogenase (E.C. 1.2.1.10) activity.

Abstract: Provided are antisense oligomers targeted against or genes associated with a biochemical pathway and/or cellular process, and related compositions and methods of using the oligomers and compositions to treat an infected mammalian subject, for example, as primary antimicrobials or as adjunctive therapies with classic antimicrobials.

Abstract: The present invention relates in part to nucleic acids, including nucleic acids encoding proteins, therapeutics and cosmetics comprising nucleic acids, methods for delivering nucleic acids to cells, tissues, organs, and patients, methods for inducing cells to express proteins using nucleic acids, methods, kits and devices for transfecting, gene editing, and reprogramming cells, and cells, organisms, therapeutics, and cosmetics produced using these methods, kits, and devices.

Abstract: The present invention relates to methods for constructing a filamentous fungal strain for production of multiple recombinant polypeptides having biological activity. The present invention also relates to methods for producing multiple recombinant polypeptides having biological activity in a filamentous fungal strain. The present invention also relates to filamentous fungal strains expressing multiple recombinant polypeptides having biological activity.

Abstract: The present invention provides multiplex assays, methods and kits that may be used to detect and confirm the presence of MRSA in a sample. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes. The present invention further comprises assays useful to identify and differentiate MRSA, MSSA, MRSE, MSSE, MRCNS and MSCNS in a sample.

Abstract: The present invention relates to compositions involving randomized in-frame fusion polynucleotides and their introduction into a host organism to identify desirable phenotypic changes. The present invention further relates to methods of generating these randomized in-frame fusion polynucleotides by introducing randomized in-frame fusion polynucleotides into an organism, selecting for organisms with new or altered phenotypes, re-isolating the randomized in-frame fusion polynucleotides from the selected organisms, re-assembling the constituent polynucleotides of the re-isolated randomized in-frame fusion polynucleotides into new collections of randomized in-frame fusion polynucleotides, and repeating the selection for organisms with new or altered phenotypes.

Abstract: The invention is directed to variant glucoamylases as compared to SEQ ID NO:1, including amino acid substitutions at positions including 24, 32, 47, 71, 75, 88, 102, 104, 114, 118, 190, 201, 204, 260, 228, 230, 269, 271, 272, 281, 283, 284, 285, 293, 350, 313, 321, 338, 343, 367, 371, 386, 372, 401, 408, 420, 448, 463, 483, 484, 507, 530, 563 599 and 605 that retain glucoamylase activity.

Abstract: A method for producing heparosan is provided. Heparosan is produced by culturing an Escherichia bacterium having a heparosan-producing ability and modified so that expression of one or more genes, such as rbsR, rbsK, rbsB, hsrA, glgB, glgX, micF, rcsD, rcsB, ybiX, ybiI, ybiJ, ybiC, ybiB, rfaH, nusG, pcoR, pcoS, pcoE, yhcN, yhcO, aaeB, aaeA, aaeX, g1455, alpA, g1453, yrbA, mlaB, mlaC, mlaD, mlaE, mlaF, yrbG, norW, ybjI, ybjJ, ybjK, rybB, yjjY, yjtD, thrL, thrA, thrB, fruA, psuK, ytfT, yjfF, fbp, yagU, paoA, paoB, gsiC, gsiD, yliE, irp2, irp1, bhsA, ycfS, lepB, rnc, era, dapA, gcvR, bcp, hyfA, rpoE, nadB, yfiC, srmB, g1414, g1413, nuoE, nuoF, nuoG, glmZ, hemY, hemX, hemD, rlmL, artQ, artM, artJ, rlmC, ybjO, yejO, yejM, yejL, rpoS, ygbN, ygbM, ygbL, g3798, g3797, g3796, g3795, g3794, g3793, g3792, ryjA, soxR, soxS, yjcC, yjcB, efeU, and efeO, is/are increased in a medium, and collecting heparosan from the medium.

Abstract: Provided are a vector replicable in E. coli and a cell of the genus Komagataeibacter, a cell including the same, a method of producing a target protein using the cell, or a method of evaluating a candidate promoter using the cell.

Abstract: The present invention provides a method, a kit and composition for determining MRSA and other Staphylococcus strain resistance to one or more antibiotic agents through detecting the presence of the respective antibiotic resistance gene. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Abstract: Fungi, such as Aspergillus niger, having a dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase (Alg3) gene genetic inactivation, increased expression of a loss of aflR expression A (LaeA), or both, are described. In some examples, such mutants have several phenotypes, including an increased production of citric acid relative to the parental strain. Methods of using the disclosed fungi to make citric acid are also described, as are compositions and kits including the disclosed fungi. Further described are Aspergillus terreus fungi overexpressing the LaeA gene and the use of such fungi for the production of itaconic acid.

Abstract: Sequences of novel adeno-associated virus capsids and vectors and host cells containing these sequences are provided. Also described are methods of using such host cells and vectors in production of rAAV particles. AAV-mediated delivery of therapeutic and immunogenic genes using the vectors of the invention is also provided.

Abstract: Described are compositions and methods relating to variant filamentous fungi having altered growth characteristics. Such variants are well-suited for growth in submerged cultures, e.g., for the large-scale production of enzymes and other proteins for commercial applications.

Abstract: Provided herein are methods and compositions for expression of a nucleic acid construct comprising nucleic acids encoding a) a recombinant polypeptide, and b) a prototrophy-restoring enzyme in a host cell that is auxotrophic for at least one metabolite. In various embodiments, the host cell is auxotrophic for a nitrogenous base compound or an amino acid. The invention involves introducing an analog into the growth media for the host cell such that the analog is incorporated into the recombinant polypeptide or a nucleic acid coding sequence thereof. In various embodiments, the compositions and methods disclosed herein result in improved recombinant protein expression compared to expression of recombinant protein in an antibiotic selection system, or compared to expression of the recombinant protein in an expression system that lacks a metabolite analog.

Abstract: A splice variant of bcr-abl mRNA that produces BCR-ABL protein with a truncated C-terminus and its role in resistance to treatment with kinase inhibitors is disclosed. Vectors for expressing the truncated gene product are provided as well as recombinant cells that express the truncated gene product from a cDNA construct. Also provided are methods compositions and kits for detecting the BCR-ABL splice variant. Additionally, methods for screening BCR-ABL kinase domain inhibitors which rely on the recombinant cells and methods of predicting likelihood for resistance of a CML patient with a BCR/ABL translocation respond to treatment with one or more BCR-ABL kinase inhibitors are also disclosed.

Abstract: Embodiments provided herein generally relate to methods and materials for ultrasound-mediated introduction of exogenous substances into microorganisms. Some embodiments relate to methods of introducing an exogenous material into a microorganism such as an algae. The methods can include, for example, providing a microorganism (e.g., algae); providing a population of bubbles that comprise one or more nucleic acid molecules and/or one or more polypeptide or one or more protein molecules; contacting the population of bubbles with the algae; applying ultrasound to the bubbles and algae with sufficient energy to cavitate one or more of bubbles comprising the one or more nucleic acid molecules in proximity to the algae; and maintaining the algae and the one or more burst bubbles comprising the one or more nucleic acid molecules in contact for a period of time sufficient to permit entry of at least one nucleic acid molecule into the algae.

Abstract: A synergistic antimicrobial composition containing lenacil and flurochloridone is provided. Also provided is a method of inhibiting the growth of or controlling the growth of microorganisms in a building material by adding such a synergistic antimicrobial composition. Also provided is a coating composition containing such a synergistic antimicrobial composition, and a dry film made from such a coating composition.

Abstract: Provided herein are methods for cleaving a target RNA polynucleotide. The target RNA polynucleotide includes a Cas6 recognition domain and a cleavage site, and may be based on a repeat from a CRISPR locus. The methods may be practiced in vivo or in vitro. Also provided are polypeptides that have Cas6 endoribonuclease activity in the presence of a target RNA polynucleotide, and methods for using the polypeptides.

Abstract: Provided is a method of simultaneous co-integration of multiple nucleic acid sequences into a microbial organism comprising culturing a microbial organism to be transformed until a growth phase is reached in which a random integration is facilitated; and transforming the microbial organism by mixing the cultured microbial organism with a sample to be co-integrated into the microbial organism with, wherein the sample comprises more than one nucleic acid sequence, and the products generated from the method.

Abstract: The present invention provides an array for rapidly identifying a host cell population capable of producing a heterologous protein with improved yield and/or quality. The array comprises one or more host cell populations that have been genetically modified to increase the expression of one or more target genes involved in protein production, decrease the expression of one or more target genes involved in protein degradation, or both. One or more of the strains in the array may express the heterologous protein of interest in a periplasm compartment or may secrete the heterologous protein extracellularly through an outer cell wall. The strain arrays are useful for screening for improved expression of any protein of interest including therapeutic proteins, hormones, growth factors, extracellular receptors or ligands, proteases, kinases, blood proteins, chemokines, cytokines, antibodies and the like.

Abstract: The disclosure relates to a process of obtaining a fully folded two chain insulin glargine that require no further processing to make it functionally active. The present disclosure discloses a surprising effect of over expression of Kex2p intracellularly under the control of inducible FLD1 promoter in the host Pichia pastoris to produce two chain functional glargine secreted directly in the medium. The schematic diagram of how the two chains are made inside the host Pichia pastoris and secretes into the medium.

Abstract: Provided herein are recombinant yeast cells having an active 3-Hydroxypropionic Acid (3-HP) pathway and further comprising a heterologous polynucleotide encoding a non-phosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN). Also described are methods of using the recombinant yeast cells to produce 3-HP and acrylic acid.

Abstract: The present invention relates to peptides, nucleic acids and methods for transforming a bacterium belonging to the Streptococcus genus by natural competence and their use in the food and feed industry.

Abstract: Herein a Bacillus exosporium molecule delivery (BEMD) system that provides a means to deliver molecules of interest (MOIs) to an environment is disclosed. The system results in the display of MOIs on the exosporium surface of Bacillus family members such that they can be delivered to an environment in a stable and active form. In addition, methods of making and using the system are described.

Abstract: Recombinant DNA techniques are used to produce oleaginous recombinant cells that produce triglyceride oils having desired fatty acid profiles and regiospecific or stereospecific profiles. Genes manipulated include those encoding stearoyl-ACP desturase, delta 12 fatty acid desaturase, acyl-ACP thioesterase, ketoacyl-ACP synthase, and lysophosphatidic acid acyltransferase. The oil produced can have enhanced oxidative or thermal stability, or can be useful as a frying oil, shortening, roll-in shortening, tempering fat, cocoa butter replacement, as a lubricant, or as a feedstock for various chemical processes. The fatty acid profile can be enriched in midchain profiles or the oil can be enriched in triglycerides of the saturated-unsaturated-saturated type.

Abstract: Methods for producing biliverdin in a microorganism, methods for producing biliverdin from a non-animal source, cells for producing biliverdin and methods for producing cells for producing biliverdin are disclosed.

Abstract: The invention provides non-naturally occurring microbial organisms having a 4-hydroxybutyrate, 1,4-butanediol, or other product pathway and being capable of producing 4-hydroxybutyrate, 1,4-butanediol, or other product, wherein the microbial organism comprises one or more genetic modifications. The invention additionally provides methods of producing 4-hydroxybutyrate, 1,4-butanediol, or other product or related products using the microbial organisms.

Abstract: Disclosed herein is a microorganism capable of producing ethane-1,2-diol from D-xylose, and a method for producing ethane-1,2-diol using the same. More specifically, the present invention relates to an engineered Escherichia coli (E. coli) prepared by knocking out a D-xylose isomerase gene and/or an aldehyde dehydrogenase gene within the genomic DNA of E. coli and transforming an expression vector including a D-xylose dehydrogenase gene into the E. coli, and an efficient method for producing ethane-1,2-diol from D-xylose using the engineered E. coli.

Abstract: This invention relates to the field of biotechnology or genetic engineering. Specifically, this invention relates to the field of gene expression. More specifically, this invention relates to a novel ecdysone receptor/chimeric retinoid X receptor-based inducible gene expression system and methods of modulating gene expression in a host cell for applications such as gene therapy, large-scale production of proteins and antibodies, cell-based high throughput screening assays, functional genomics and regulation of traits in transgenic organisms.

Abstract: Methods and compositions for targeted delivery of biotherapeutics are provided. The compositions comprise bile-sensitive St. thermophilus bacteria modified to release a biotherapeutic agent following bile exposure. Biotherapeutic agents released by the St. thermophilus bacteria disclosed herein include AQ and AQR rich peptides. Methods of the invention comprise administering to a subject a St. thermophilus bacterium modified to release a biotherapeutic agent following bile exposure. Administration of the St. thermophilus bacterium promotes a desired therapeutic response. The bacterium may be modified to express and release AQ or AQR rich peptides which subsequently inhibit cellular apoptosis or reduce mucosal damage. Thus, methods of the invention find use in treating or preventing a variety of gastrointestinal disorders including C. difficile infection and antibiotic-associated diarrhea.

Abstract: Methods of simultaneously excising large nucleic acid sequences from a target nucleic acid and inserting large foreign nucleic sequences into the target nucleic acid sequence using DNA binding protein nucleases are described.

Abstract: A genetically engineered yeast cell capable of producing lactate having increased TPI activity, a method of preparing the yeast cell, and a method of producing lactate by using the yeast cell.

Abstract: This disclosure describes engineered biosynthetic pathways, recombinant cells, and methods relating to biosynthesis of esters. The recombinant cells may be modified to exhibit increased biosynthesis of an ester compared to a wild-type control. The recombinant cell may be incubated in medium that includes a carbon source under conditions effective for the recombinant cell to produce an ester. This disclosure also describes a method that generally includes introducing into a host cell a heterologous polynucleotide encoding at least one polypeptide that catalyzes a step in converting a carbon source to an ester, wherein the at least one polynucleotide is operably linked to a promoter so that the modified host cell catalyzes conversion of the carbon source to an ester.

Abstract: The present invention encompasses a phototrophic microorganism with altered and controlled adhesive properties. One aspect of the present invention encompasses a genetically modified phototrophic microorganism capable of controlled adhesion. The microorganism comprises a recombinant nucleic acid construct, wherein the nucleic acid construct comprises an inducible promoter operably-linked to a nucleic acid encoding an adhesion protein.

Abstract: Isolated mutant Mycobacterium tuberculosis bacteria comprising a deletion in the ESAT-6 gene cluster region 3 (esx-3 region) are provided, as well as compositions comprising such, methods of production thereof and methods of use thereof.

Abstract: Provided is a genetically engineered yeast cell with lactate production capacity, including an enzyme that catalyzes conversion of acetaldehyde to acetyl-CoA and an enzyme that catalyzes conversion of pyruvate to lactate, which activities are increased compared to a parent cell of the yeast cell, as well as a method of producing the genetically engineered yeast cell and method of producing lactate using the genetically engineered yeast cell.

Abstract: A recombinant microorganism is provided herein, in particular, a recombinant microorganism of the Azotobacteraceae family. The recombinant Azotobacter microorganism is capable of fixing atmospheric nitrogen continuously in the presence of oxygen and externally fixed nitrogen sources. The present invention further provides a process for production of the recombinant microorganism and a composition comprising the recombinant microorganism for use as biofertilizers and/or for use in the preparation of a fertilizer composition. The recombinant microorganism produced by this invention is an environmental friendly, highly beneficial microorganism.

Abstract: Rationally-designed LAGLIDADG meganucleases and methods of making such meganucleases are provided. In addition, methods are provided for using the meganucleases to generate recombinant cells and organisms having a desired DNA sequence inserted into a limited number of loci within the genome, as well as methods of gene therapy, for treatment of pathogenic infections, and for in vitro applications in diagnostics and research.