Abstract: Embodiments of the present invention concerns methods and compositions for the construction of a series of vectors containing a chemical sensing module to assess the production of a chemical compound by a microorganism.

Abstract: A phage display system is provided comprising a mutant phage-infected host cell adapted to express a peptide of interest fused to a phage capsid protein, wherein the mutant phage includes a nonsense mutation which prevents expression of the capsid protein as a functional protein, and wherein expression of the peptide of interest is controlled by an inducible repressor and by a suppressor that suppresses the nonsense mutation.

Abstract: The invention relates to compositions containing polynucleotide vectors capable of expressing a nucleic acid encoding a fusion polypeptide on the surface of a viral particle and/or a eukaryotic cell.

Abstract: The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

Abstract: The present disclosure relates to methods for efficient synthesis, cloning, transformation and screening of large diverse libraries of polynucleotide variants comprising well-defined nucleotide differences relative to a reference polynucleotide.

Abstract: Methods and systems for processing a first solution on a respective primary area of a device with a plurality of primary areas and a plurality of secondary areas are described. A method includes providing the device and dispensing a second solution to a respective secondary area of one or more secondary areas adjacent to the respective primary area, thereby mixing the first solution on the respective secondary area and the second solution on the respective primary area. The method also includes removing at least a portion of the mixed solution.

Abstract: The invention provides methods, compositions and kits for the detection and treatment of pancreatic cancer.

Abstract: Methods for screening libraries of polypeptides for biologically activity on cells. For example, polypeptides can be synthesized and encapsulated along with their coding sequences in microcapsules of an emulsion. Emulsion microcapsules can then be fused with microcapsules comprising test cells and biological activity on the cells is assessed to identify biologically active polypeptides and nucleic acid molecules encoding the same.

Abstract: Surface modifications to sensors in an array give the sensors different functionalities for adsorbing or binding molecules. A first sensor in the array includes a first resonating member having a first surface comprising a polymer receptor material coated over a first underlying material. A second sensor includes a second resonating member having a second surface comprising the polymer receptor material coated over a second underlying material that is different than the first underlying material. The first underlying material, the second underlying material, and the polymer receptor material are selected such that the first resonating member, having a combination of the polymer receptor material and the first underlying material, has a different ability to adsorb or bind a mass of one or more analytes than does the second resonating member having a combination of the polymer receptor material with the second underlying material. Methods for fabricating sensors with surface modifications are also provided.

Abstract: Patterned material depositions are formed on a surface of a substrate following filling each of one or more dispersions between each of spaces bounded by a stencil or a pair of patterned barriers on the surface of the substrate. Each dispersion comprises at least one liquid continuous medium and at least one dispersed material. Each patterned material deposition encompasses at least one dispersed material and is formed by evaporating the liquid continuous medium from the dispersion. Patterned material depositions may have multilayer structures. Systems include methods and device.

Abstract: Disclosed is a serum-free freezing medium used in adipose-derived stem cells and a method for establishing an adipose-derived stem cell library. The serum-free freezing medium comprises a serum-free culture medium, dimethyl sulfoxide and a serum substitution component KSR; the defects of unstable freezing quality of the adipose-derived stem cells and influence of harmful factors in serum on the adipose-derived stem cells are solved, and the adipose-derived stem cells stored have the advantages of high survival percentage, well adherence growth and strong differentiation capacity.

Abstract: The invention refers to a library of bidirectional expression cassettes or expression vectors comprising a repertoire of bidirectional promoter sequences, each expression cassette comprising a promoter sequence operably linked to a first gene in one direction, and operably linked to an oppositely oriented second gene in the other direction which is different from the first gene, and bidirectional Pichia pastoris or CHO cells promoter sequences. The invention further refers to a method of screening or selecting a bidirectional promoter suitable for expressing at least two GOI in a host cell and a kit comprising a) an expression cassette consisting of the first and second genes and a stuffer sequence separating them, which stuffer sequence comprises a recognition site for a type IIS restriction enzyme at both ends; b) the type IIS restriction enzyme; c) and a repertoire of promoter, preferably a promoter library including bidirectional promoters.

Abstract: A photonic crystal-immunoassay platform wherein the periodicity of wells in an array are designed based on the leaky wave-guided modes of high refractive index material and a wavelength of excitation and/or emission of electromagnetic radiation associated with a signal used in the assay.

Abstract: Methods and apparatuses for generating microscopic patterns of macromolecules such as proteins on a solid surface are described. Pulsed laser light is used to alter surface portions of a solid surface substrate in a predetermined pattern, by removing macromolecules from surface portions of the substrate where the light is focused. The same wavelength light at lower intensity can be used to visualize the removal by its reflection from the specimen surface along the path to the detector. Select macromolecules introduced to the substrate selectively adhere to select surface portions, thereby depositing macromolecules in the predetermined pattern on the solid surface.

Abstract: A proteinaceous particle, for example a bacteriophage, ribosome or cell, displaying on its surface a T-cell receptor (TCR). The displayed TCR is preferably a heterodimer having a non-native disulfide bond between constant domain residues. Such display particles may be used for the creation of diverse TCR libraries for the identification of high affinity TCRs. Several high affinities are disclosed.

Abstract: A sensor array includes resonator sensors having respective receptor materials disposed thereon. The receptor materials have a physical property relevant to their ability to bind or adsorb one or more analytes in a sample. The physical property of the receptor materials on the sensors systematically increases or decreases in degree from one sensor to the next in the array. The device also comprises at least one detector for detecting sensor responses when masses of the analytes are adsorbed or bound to the receptor materials on the sensors. With this graded panel of sensors in the array, the analytes may adsorb or bind to the functionalized sensors with a pattern of responses specific to each analyte.

Abstract: This invention provides transcription regulatory control sequences, the activity of which function as biomarkers for a variety of biological responses. This invention also provides expression constructs in which a biomarker transcription regulatory sequence is operably linked with a sequence for a reporter. Cells that comprise these expression constructs can be used in assays to identify conditions that modulate activity of the biological response.

Abstract: The present disclosure provides adeno-associated virus (AAV) virions with altered capsid protein, where the AAV virions exhibit greater infectivity of retinal cells, when administered via intravitreal injection, compared to wild-type AAV. The present disclosure further provides methods of delivering a gene product to a retinal cell in an individual, and methods of treating ocular disease.

Abstract: The present disclosure relates general to devices, systems, and methods of using such devices in creating and handling hanging drops of fluid. The present disclosure also relates to cell culture devices, methods and/or systems of using such devices as well as the use of cell culture devices, for example, for research and high throughput screening.

Abstract: A generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening is disclosed. For example, selective biotinylation of phage particles and yeast cells displaying a binder to any given target can be achieved via application of a coupled enzyme reaction that includes a peroxidase, an oxidase and a catalase.

Abstract: The present invention relates to antibodies (including anti-B7-H4 antibodies) and their antigen-binding fragments and to other molecules (including fusion proteins that bind to the cognate antigen/receptor, etc.) that are capable of immunospecifically binding to B7-H4 and the uses of such molecules in the diagnosis and the treatment of cancer and other diseases. The invention particularly concerns the use of such molecules to retard or prevent tumor growth, inhibit tumor-mediated suppression, eliminate tumors and/or deplete or block the activity of tumor associated macrophages (“TAMs”) so as to alter their activity and/or decrease TAM—mediated immune suppression.

Abstract: A proteinaceous particle, for example a bacteriophage, ribosome or cell, displaying on its surface a T-cell receptor (TCR). The displayed TCR is preferably a heterodimer having a non-native disulfide bond between constant domain residues. Such display particles may be used for the creation of diverse TCR libraries for the identification of high affinity TCRs. Several high affinities are disclosed.

Abstract: The disclosure relates to devices, systems and methods that address the variability in immunohistochemistry (IHC) tests that can lead to inaccurate diagnosis or misdiagnosis while maintaining important structural information within the specimen. The devices may include a control region having a control unit including a plurality of substantially homogenous samples and a biological sample region.

Abstract: The present invention relates, inter alia, to polyspecificity reagents, methods of making the same, and methods of using the same in, inter alia, the selection, screening, enrichment, and identification of non-polyspecific, and thus developable, polypeptides.

Abstract: Embodiments of the present disclosure provide for arrays, systems, and methods analyzing cells, methods of making arrays, and the like.

Abstract: The present invention relates to single cell array micro-chips and fabrication, electrical measurement and electroporation method thereof. The single cell array microchip comprises a substrate (1), a plurality of positioning electrodes (2) formed in an array, a plurality of measuring electrode-pairs (3) formed in an array, and a micro sample pool (4). The invention integrates cell array positioning with electrical measurement and electroporation for living cells, which is characteristic of label-free and noninvasive methods to manipulate, position particles/cells as well as further measure their electrical parameters. Therefore, single-cell-array positioning and multi-mode in-situ real-time measurement can be realized for intensive analysis. Since the positioned cells are immobile, the precision of the electrical measurement of cells is effectively improved, so is the efficiency of electroporation with lower cell mortality rate.

Abstract: The present invention relates to a method for the preparation of a library of host cells, a plurality of which comprise an assembled polynucleotide at a target locus, which method comprises: (a) providing a plurality of polynucleotides comprising two or more polynucleotide subgroups, wherein: (i) a plurality of polynucleotides in each polynucleotide subgroup comprises sequence encoding a peptide or polypeptide and/or a regulatory sequence; (ii) a plurality of peptides or polypeptides encoded by, or a plurality of regulatory sequences comprised within, each polynucleotide subgroup share an activity and/or function; (iii) at least one polynucleotide subgroup comprises at least two non-identical polynucleotide species; (iv) a plurality of polynucleotides of each polynucleotide subgroup comprises sequence enabling homologous recombination with a plurality of polynucleotides from one or more other polynucleotide subgroups; and (v) a plurality of polynucleotides in two polynucleotide subgroups comprise a nucleotide

Abstract: A method of patterning a surface of a substrate comprising: (a) applying a coating to the surface to form a coated surface, and (b) treating the coated surface with a patterned microplasma comprising a plurality of localised microplasma discharges such that localised regions of the coated surface are selectively exposed to the localised microplasma discharges to form exposed localised regions and unexposed regions that have not been substantially exposed to a microplasma discharge; wherein the coating at the exposed localised regions is modified by the patterned microplasma and the coating at the unexposed regions is substantially unmodified to form a patterned surface on the substrate.

Abstract: The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites with unique specificity. The methods permit the simultaneous cloning of two or more different nucleic acid molecules. In some embodiments the molecules are fused together while in other embodiments the molecules are inserted into distinct sites in a vector. The invention also generally provides for linking or joining through recombination a number of molecules and/or compounds (e.g., chemical compounds, drugs, proteins or peptides, lipids, nucleic acids, carbohydrates, etc.) which may be the same or different. Such molecules and/or compounds or combinations of such molecules and/or compounds can also be bound through recombination to various structures or supports according to the invention.

Abstract: Methods and compositions are provided for studying and targeting RNA structures. In particular, antibodies and antibody fragments that contain an Fab were produced. Phage display libraries that were engineered to produce RNA-specific antibody and antibody fragments were made. Antibodies, or fragments thereof, that have at least one Fab that specifically binds tRNAiMet, the P4-P6 domain of Tetrahymena Group I intron, the glycine riboswitch from Vibrio Cholerae, or the glycine riboswitch from Fusobacterium Nucleatum were identified. The production of these RNA-specific antibodies and antibody fragments can be used to study the structure of the RNA as well as to treat diseases with known RNA targets. For example, an Fab specific to tRNAiMet was produced that can be used to treat cancer in subjects where tRNAiMet is overexpressed.

Abstract: Engineered, living, three-dimensional liver tissue constructs comprising: one or more layers, wherein each layer contains one or more liver cell types, the one or more layers cohered to form a living, three-dimensional liver tissue construct. In some embodiments, the constructs are characterized by having at least one of: at least one layer comprising a plurality of cell types, the cell types spatially arranged relative to each other to create a planar geometry; and a plurality of layers, at least one layer compositionally or architecturally distinct from at least one other layer to create a laminar geometry. Also disclosed are arrays and methods of making the same. Also disclosed are engineered, living, three-dimensional liver tissue constructs for use in the augmentation or restoration of one or more liver functions, by in vivo delivery of tissue or utilization of tissue in an extracorporeal device.

Abstract: Device for use in a biosensor comprising a multisite array of test sites, the device being useful for modulating the binding interactions between a (biomolecular) probe or detection agent and an analyte of interest from a biological by modulating the pH or ionic gradient near the electrodes in such biosensor. The device provides a biosensor which is more accurate, reliable and the results of which are more reproducible. Analytic methods for more accurately measuring an analyte of interest in a biological sample are also provided.

Abstract: Embodiments described herein relate to methods, devices, and computer systems thereof for the derivation of T CAR libraries (Universal Subject or Individual Subject) for personalized treatment of disease in a subject. In certain embodiments, differential screening of normal and diseased tissue expression data is utilized to determine disease-specific antigens and thereby generate T CAR cells reactive to such antigens to form a disease-specific library. In certain embodiments, determination of the most effective T CAR clones from the disease-specific library is based on the subject's own disease-specific antigens. In certain embodiments, a subject is treated with a therapeutically effective amount of T CAR clones.

Abstract: Decoy nucleic acid sequences comprising a binding site for a target transcription factor, wherein the binding site is not operably linked to a gene, and wherein the transcription factor comprises a regulator of expression of a gene or genes in Clostridium difficile encoding one or more of: (i) a cellular growth factor; (ii) a cellular toxin; (iii) a cellular sporulation factor; (iv) a cellular stress response; and/or (v) a cellular essential gene are described. Uses of the decoys in antibacterial complexes for the treatment of bacterial infections are also described.

Abstract: Embodiments described herein relate to methods, devices, and computer systems thereof for the derivation of T CAR libraries (Universal Subject or Individual Subject) for personalized treatment of disease in a subject. In certain embodiments, differential screening of normal and diseased tissue expression data is utilized to determine disease-specific antigens and thereby generate T CAR cells reactive to such antigens to form a disease-specific library. In certain embodiments, determination of the most effective T CAR clones from the disease-specific library is based on the subject's own disease-specific antigens. In certain embodiments, a subject is treated with a therapeutically effective amount of T CAR clones.

Abstract: Engineered, living, three-dimensional liver tissue constructs comprising: one or more layers, wherein each layer contains one or more liver cell types, the one or more layers cohered to form a living, three-dimensional liver tissue construct. In some embodiments, the constructs are characterized by having at least one of: at least one layer comprising a plurality of cell types, the cell types spatially arranged relative to each other to create a planar geometry; and a plurality of layers, at least one layer compositionally or architecturally distinct from at least one other layer to create a laminar geometry. Also disclosed are arrays and methods of making the same. Also disclosed are engineered, living, three-dimensional liver tissue constructs for use in the augmentation or restoration of one or more liver functions, by in vivo delivery of tissue or utilization of tissue in an extracorporeal device.

Abstract: Disclosed herein are compositions comprising beads with unique identifiers for storing information about a multiplex assay as well as methods for using the same in multiplex chemical and biological assays.

Abstract: The invention relates to a method for generating a gene mosaic by somatic in vivo recombination, comprising a) in a single step procedure (i) transforming a cell with at least one gene A having a sequence homology of less than 99.5% to another gene to be recombined that is an integral part of the cell genome or presented in the framework of a genetic construct, (ii) recombining said genes, (iii) generating a gene mosaic of the genes at an integration site of a target genome, wherein said at least one gene A has a single flanking target sequence either at the 5? end or 3? end anchoring to the 5? or 3? end of said integration site, and b) selecting clones comprising the gene mosaic, wherein said cell is a eukaryotic strain with a knock-out of at least one DNA repair gene. The invention further refers to a method of producing a diversity of gene mosaics and gene assembly.

Abstract: The present invention comprises methods, systems and compositions comprising concentric chamber cell culture analog devices, comprising biologically functional cells, which function similarly to in vivo conditions.

Abstract: A method and device for the rapid quantification of biomolecules (320) present in a nanochannel (210) is claimed. In particular, the present invention relates to a novel concept of liquid actuation and selectively functionalized surfaces in a nanochannel that create a concentration gradient of transitory immobilized biomolecules (340) across the nanochannel. The present concept enables the quantification of biomolecular interactions of interest (320).

Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.

Abstract: The present invention provides arrays comprising polypeptides associated with viruses that are immobilized to an electrode in a directional orientation such that the surface area of the electrode and the sensitivity of the electrode is increased. The invention also provides for methods of diagnosing and/or prognosing a certain disease or disorder through contacting a sample from a patient with an array comprising the polypeptides associated with viruses.

Abstract: Apparatus, systems, and methods for detecting, screening and sampling of cells are disclosed.

Abstract: Provided are protein, nucleic acid, and cellular libraries of multivalent binding proteins (e.g., DVD-Fab or DVD-Ig molecules) and the use of these libraries for the screening of multivalent binding proteins using cell surface display technology (e.g., yeast display).

Abstract: The present invention generally relates to bacterial polypeptide display systems, libraries using these bacterial display systems, and methods of making and using these systems, including methods for improved display of polypeptides on the extracellular surface of bacteria using circularly permuted transmembrane bacterial polypeptides that have been modified to increase resistance to protease degradation and to enhance polypeptide display characteristics.

Abstract: The invention relates generally to polypeptides, such as antibody molecules, that demonstrate high stability and solubility. In particular, the invention relates to polypeptides comprising paired VL and VH domains that demonstrate soluble expression and folding in a reducing or intracellular environment. The invention also relates to polynucleotides encoding such polypeptides, to libraries of such polypeptides or polynucleotides, and to methods of using such polypeptides in research, diagnostic and therapeutic applications.

Abstract: A layered, microfluidic living cell array is disclosed. The cell array comprises a first layer comprising at least one cell culture channel; a second layer comprising at least one microfluidic channel; and a third layer, disposed between the first layer and the second layer. The third layer comprises a filter membrane with a plurality of pores, each pore fluidly connecting the microfluidic channel to the cell culture channel.

Abstract: The present invention is related to genomic nucleotide sequencing. In particular, the invention describes a paired end sequencing method that improves the yield of long-distance genomic read pairs by constructing long-insert clone libraries (i.e., for example, a fosIll library or a fosCN library) and converting the long-insert clone library using inverse polymerase chain reaction amplification or shearing and recircularization of shortened fragments into a library of co-ligated clone-insert ends. The resultant jumping libraries are compatible with massively parallel sequencing techniques. The compositions and methods disclosed herein contemplate sequencing complex genomes as well as detecting chromosomal structural rearrangements.

Abstract: Viable Gram-negative bacteria or components thereof comprising outer membranes that substantially lack a ligand, such as Lipid A or 6-acyl lipidpolysaccharide, that acts as an agonist of TLR4/MD-2. The bacteria may comprise reduced activity of arabinose-5-phosphate isomerases and one or more suppressor mutations, for example in a transporter thereby increasing the transporter's capacity to transport lipid IVA or in membrane protein YhjD. One or more genes (e.g., lpxL, lpxM, pagP, lpxP, and/or eptA) may be substantially deleted and/or one or more enzymes (e.g., LpxL, LpxM, PagP, LpxP, and/or EptA) may be substantially inactive. The bacteria may be competent to take up extracellular DNA, may be donor bacteria, or may be members of a library. The present invention also features methods of creating and utilizing such bacteria.

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity. The libraries are designed to reflect the preimmune repertoire naturally created by the human immune system, with or without DH segments derived from other species, and are based on rational design informed by examination of publicly available databases of antibody sequences.