Abstract: Described herein are methods and vectors for rational, multiplexed manipulation of chromosomes within open reading frames (e.g., in protein libraries) or any segment of a chromosome in a cell or population of cells, in which various CRISPR systems are used.

Abstract: This disclosure relates to a chimeric antigen receptor for binding with a target antigen. The chimeric antigen receptor comprises at least one antigen specific targeting region including a multispecific antibody evolved from a wild-type antibody or a fragment thereof and having at least one of: (a) a decrease in activity in the assay at the normal physiological condition compared to the wild-type antibody or the fragment thereof, and (b) an increase in activity in the assay under the aberrant condition compared to the wild-type antibody or the fragment thereof. A method for using the chimeric antigen receptor and cytotoxic cells for cancer treatment is also provided. A method for producing the chimeric antigen receptor is also provided.

Abstract: Provided herein is a method for fabricating transformable or transfectable molecules that includes an assembly reaction containing a variety of pre-made cassettes possessing ends that hybridize to one another, transforming or transfecting said molecules into a desired host cell and then selecting a transformed/transfected host cell containing plasmid molecules composed of said the cassettes. A kit for performing the method is also provided.

Abstract: A passive, hydrodynamic technique implemented using a microfluidic device to perform co-encapsulation of samples in droplets and sorting of said droplets is described herein. The hydrodynamic technique utilizes laminar flows and high shear liquid-liquid interfaces at a microfluidic junction to encapsulate samples in the droplets. A sorting mechanism is implemented to separate sample droplets from empty droplets. This technique can achieve a one-one-one encapsulation efficiency of about 80% and can significantly improve the droplet sequencing and related applications in single cell genomics and proteomics.

Abstract: A microelectrode for electroporating an individual cell or embryo that includes a substrate with an electrically insulated surface, a first electrode adjacent to the electrically insulated surface of the substrate, a second electrode adjacent to the electrically insulated surface of the substrate and separated from the first electrode a predetermined distance so as to form a channel, and a liquid medium situated within the channel. The liquid medium is capable of fluidic transport of the cell or embryo through or into the channel and capable of supporting an electric field. The first and second electrodes include surfaces substantially orthogonal to the electrically insulated surface of the substrate with an edge length that is less than or equal to a diameter of the cell or embryo. The predetermined distance may be 50% to 200% of the diameter of the cell or embryo.

Abstract: The present invention relates in part to nucleic acids encoding proteins, therapeutics comprising nucleic acids encoding proteins, methods for inducing cells to express proteins using nucleic acids, methods, kits and devices for transfecting, gene editing, and reprogramming cells, and cells, organisms, and therapeutics produced using these methods, kits, and devices. Methods and products for altering the DNA sequence of a cell are described, as are methods and products for inducing cells to express proteins using synthetic RNA molecules. Therapeutics comprising nucleic acids encoding gene-editing proteins are also described.

Abstract: Methods and compositions are provided for making one or more targeted genetic modifications at a target genomic locus within a cell and for producing non-human animals comprising the modified genomic locus. The methods employ two or more large targeting vectors which are capable of recombining with each other and with the target genomic locus in a single genomic targeting step. The methods may also be employed in combination with a nuclease agent. Methods and compositions are also provided for enhancing homologous recombination at a target genomic locus in a cell. The methods employ two or more nucleic acids comprising one or more overlapping sequences. The methods may be employed in combination with a nuclease agent or without a nuclease agent.

Abstract: The present invention discloses a genus of insect inhibitory proteins that exhibit properties directed to controlling Lepidopteran and/or Hemipteran crop pests, methods of using such proteins, nucleotide sequences encoding such proteins, methods of detecting and isolating such proteins, and their use in agricultural systems.

Abstract: Genetically modified non-human animals and methods and compositions for making and using them are provided, wherein the genetic modification comprises a deletion in an immunoglobulin constant region CH1 gene (optionally a deletion in a hinge region) of an IgG, IgA, IgD, and/or IgE, and wherein the mouse is capable of expressing a functional IgM. Genetically modified mice are described, including mice having a functional IgM gene and modified to have a deletion of a CH1 domain and a hinge region in a heavy chain constant domain that is not an IgM, e.g., in an IgG heavy chain constant domain. Genetically modified mice that make human variable/mouse constant chimeric heavy chain antibodies (antibodies that lack a light chain), fully mouse heavy chain antibodies, or fully human heavy chain antibodies are provided.

Abstract: Genetically modified non-human animals are provided that express an immunoglobulin variable domain that comprises at least one histidine, wherein the at least one histidine is encoded by a substitution of a non-histidine codon in the germline of the animal with a histidine codon, or the insertion of a histidine codon in a germline immunoglobulin nucleic acid sequence. Immunoglobulin genes comprising histidines in one or more CDRs, in an N-terminal region, and/or in a loop 4 region are also provided. Immunoglobulin variable domains comprising one or more histidines (e.g., histidine clusters) substituted for non-antigen-binding non-histidine residues. Non-human animals that are progeny of animals comprising modified heavy chain variable loci (V, D, J segments), modified light chain variable loci (V, J segments), and rearranged germline light chain genes (VJ sequences) are also provided. Non-human animals that make immunoglobulin domains that bind antigens in a pH-sensitive manner are provided.

Abstract: The current invention relates to development of new formulation containing gold nanoparticles (AuNPs) with bi-functional recombinant fusion proteins TRAF(C) for the delivery of anticancer drugs and nucleic acids to HER2+ cancers. Using the combinatorial approach, we designed gold nanoparticle-based targeted drug delivery system (TDDS) or (Au-TR-DX-si) by combining AuNPs with bi-functional recombinant fusion protein TRAF(C) (TR), doxorubicin (DX) and siRNA (si). The recombinant protein based gold nanoparticles formulations are stable and homogenous as revealed by several physicochemical studies. In addition, the engineered fusion protein TRAF (C) has the ability to target selectively to HER2+ receptors overexpressed in ovarian cancer cells (SK-OV-3).

Abstract: The present invention relates in part to nucleic acids encoding proteins, therapeutics comprising nucleic acids encoding proteins, methods for inducing cells to express proteins using nucleic acids, methods, kits and devices for transfecting, gene editing, and reprogramming cells, and cells, organisms, and therapeutics produced using these methods, kits, and devices. Methods and products for altering the DNA sequence of a cell are described, as are methods and products for inducing cells to express proteins using synthetic RNA molecules. Therapeutics comprising nucleic acids encoding gene-editing proteins are also described.

Abstract: The disclosure relates to a skin piercing tool for locally puncturing a human or an animal skin, comprising a piercing needle, which is embodied as solid needle, in the case of which a needle body has a proximal needle section and a distal needle section, in which a piercing tip is arranged, wherein the needle body has a needle section, which is resilient against the piercing tip in response to a compressive stress, wherein the resilient needle section is arranged on the needle body in the area of an angled needle section, in which adjacent needle sections assume an angle of less than 180° with one another. Further, a hand-held device for repeated local puncturing of a human or an animal skin is provided.

Abstract: Provided herein are compositions for improving sinus microbiota and treating sinusitis. Further provided are methods of detecting imbalance in the sinus microbiota that can be indicative of sinusitis, and methods of determining whether an individual has or is at risk of developing sinusitis, e.g., chronic sinusitis.

Abstract: Provided herein is a method for fabricating transformable or transfectable molecules that includes an assembly reaction containing a variety of pre-made cassettes possessing ends that hybridize to one another, transforming or transfecting said molecules into a desired host cell and then selecting a transformed/transfected host cell containing plasmid molecules composed of said the cassettes. A kit for performing the method is also provided.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Sirtuin (SIRT), in particular, by targeting natural antisense polynucleotides of a Sirtuin (SIRT). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Sirtuins (SIRT)s.

Abstract: The subject invention pertains to delivering a polynucleotide into a target cell, particularly, into the nucleus of the target cell. The method comprises the steps of contacting the polynucleotide with the cell and applying pressure on the polynucleotide and the cell in a manner that forces the polynucleotide into the cell. The pressure can be between about 0.1 Pa to about 50 Pa; whereas, the polynucleotide is contacted with the cell at a concentration of between about 0.1 ?M and about 100 ?M. The method can be practiced for cells in culture or cells in vivo.

Abstract: The present invention concerns a method for the detection or monitoring of cancer using a biological sample selected from blood, plasma, serum, saliva, urine from an individual, said method comprising: (a) obtaining DNA from the said biological sample; (b) digesting the DNA sample with one or more methylation-sensitive restriction enzymes; (c) quantifying or detecting a DNA sequence of interest after step (b), wherein the target sequence of interest contains at least two methylation-sensitive restriction enzyme recognition sites; and (d) comparing the level of the DNA sequence from the individual to a normal standard, to detect, prognosticate or monitor cancer.

Abstract: The present invention is in the technical field of breast cancer management, and more particularly relates to the diagnosis of breast cancer. The invention is more particularly based on the finding that specific biomarkers (olfactomedin-4, neudesin and desmoplakin) are abberantly expressed in the blood of breast cancer patients.

Abstract: The present disclosure generally relates to compositions and methods for improving the efficiency of homologous recombination. In particular, the disclosure relates to reagents and the use of such reagents.

Abstract: The invention provides genetically engineered microorganisms with modified hydrogenase activity and methods related thereto. Typically, the microorganisms are C1-fixing microorganisms with one or more disruptive mutations in a hydrogenase enzyme or a hydrogenase accessory enzyme. The microorganisms may have improved tolerance to toxins, such as acetylene, isocyanide, ammonium, or nitric oxide, improved production of products, such as ethanol, 2,3-butanediol, and isopropanol, and/or improved fixation of carbon, such as carbon derived from CO or CO2.

Abstract: The present invention relates to modified guide RNAs and their use in clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems.

Abstract: This disclosure relates to a diagnostic/prognostic assay for prostate cancer and including kits used in said assay.

Abstract: The invention provides methods for isolating large oncosomes and determining cancer metastasis based on the presence of large oncosomes and contents of the large oncosomes in a subject in need thereof. Also provided herein are methods for treating cancer metastasis by specifically targeting contents of the large oncosomes.

Abstract: Aspects of the invention provide single stranded oligonucleotides for activating or enhancing expression of hemoglobin genes (HBB, HBD, HBE1, HBG1 or HBG2). Further aspects provide compositions and kits comprising single stranded oligonucleotides for activating or enhancing expression of hemoglobin genes. Methods for modulating expression of hemoglobin genes using the single stranded oligonucleotides are also provided. Further aspects of the invention provide methods for selecting a candidate oligonucleotide for activating or enhancing expression of hemoglobin genes.

Abstract: Provided is a method of treating an individual suffering from a cancer such as breast cancer by administering to the individual a long-acting topoisomerase I inhibitor such as SN-38 or irinotecan, and correlating the level of at least one tumor marker such as CA27.29 in the individual with response of the cancer to treatment with the long-acting topoisomerase I inhibitor, to thereby provide a method for predicting and assessing the therapeutic efficacy of the treatment.

Abstract: The invention generally provides improved compositions and methods for detecting, diagnosing, prognosing, and monitoring multiple myeloma, chronic lymphocytic leukemia, or B-cell non-Hodgkin lymphoma in a subject. In particular, the invention provides methods for detecting BCMA in subjects to reliably diagnose, predict survival, or monitor multiple myeloma, chronic lymphocytic leukemia, or B-cell non-Hodgkin lymphoma in the subject.

Abstract: Provided are: a cell tray provided with a concave part for supporting a cell aggregate and a hole formed on the bottom of the concave part; and a device for producing a cell structure, said device being provided with the cell tray and a puncture part passing through the cell tray and the cell aggregate, characterized in that the puncture part passes through the cell aggregate supported by the concave part until the tip thereof intrudes into the hole.

Abstract: Systems and methods for transfection devices are contemplated for delivery of various complex macrostructures. Preferred systems and methods are suitable for mRNA reprogramming and genome editing and use mechanical force to induce uptake of the macrostructures in a target cell. Contemplated devices are able to achieve high throughput of transfected cells in remarkably short time that remain viable and are capable of producing colonies.

Abstract: The invention described herein relates to novel genes and their encoded proteins, termed Mutants Associated with Resistance to STI-571 (e.g., T315I Bu-Abl), and to diagnostic and therapeutic methods and compositions useful in the management of various cancers that express MARS. The invention further provides methods for identifying molecules that bind to and/or modulate the functional activity of MARS.

Abstract: The present invention provides methods and compositions for converting a first polypeptide into a chimeric polypeptide. The invention includes two vectors: a first vector including the sequence of the first polypeptide and a second vector including a second polypeptide. The vectors include complementary site-specific recombination motifs such that site-specific recombination between the two vectors results in the generation of a chimeric polypeptide including at least a portion of the first polypeptide and at least a portion of the second polypeptide. A site-specific recombination motif may be positioned within an intron or within a coding sequence on the first or second vector.

Abstract: Biomarkers are identified by analyzing gene expression data using support vector machines (SVM) to rank genes according to their ability to separate prostate cancer from normal tissue. Expression products of identified genes are detected in patient samples, including prostate tissue, serum, semen and urine, to screen, predict and monitor prostate cancer.

Abstract: Non-human animals, e.g., mammals, e.g., mice or rats, are provided comprising an immunoglobulin heavy chain locus that comprises a rearranged human immunoglobulin heavy chain variable region nucleotide sequence. The rearranged human immunoglobulin heavy chain variable region nucleotide sequence may be operably linked to a heavy or light chain constant region nucleic acid sequence. Also described are genetically modified non-human animals comprising an immunoglobulin light chain locus comprising one or more but less than the wild type number of human immunoglobulin light chain variable region gene segments, which may be operably linked to a light chain constant region nucleic acid sequence. Also provided are methods for obtaining nucleic acid sequences that encode immunoglobulin light chain variable domains capable of binding an antigen in the absence of a heavy chain.

Abstract: The method for distinguishing between prostate carcinoma and benign prostatic hyperplasia comprising: bringing an analyte sample containing a prostate-specific antigen (PSA) into contact with a carrier having an anti-free PSA antibody immobilized thereon, thereby binding free PSA to the anti-free PSA antibody immobilized on the carrier; thereafter bringing the carrier in which the free PSA is bound to the immobilized anti-free PSA antibody into contact with a monoclonal antibody capable of specifically recognizing a glycan in which a terminal sialic acid residue is bound to galactose through an ?(2,3) bond, thereby binding the monoclonal antibody recognizing the glycan to the free PSA bound to the anti-free PSA antibody; measuring the amount of the free PSA having an N-type glycan in which a terminal sialic acid residue is bound to galactose through an ?(2,3) bond; comparing the measured amount thus obtained with a preset cutoff value for prostate carcinoma and benign prostatic hyperplasia, thereby determinin

Abstract: A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cas6 which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualizing, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualization, transcriptional activation or repression.

Abstract: This disclosure provides compositions and methods for controlling pain. In particular the disclosure provides a method for controlling pain comprising co-administration of an NGF antagonist and a TNF? antagonist. The NGF antagonist and the TNF? antagonist can be separate molecules or part of a multifunctional polypeptide, e.g., a multispecific binding molecule that comprises an NGF antagonist domain and a TNF? antagonist domain. This disclosure also provides multifunctional polypeptides, e.g., multispecific binding molecules, comprising an NGF antagonist domain, and a TNF? antagonist domain. The method provides improved pain control. Administration of an NGF antagonist and a TNF? antagonist as provided herein can control pain in the subject more effectively than an equivalent amount of the NGF antagonist or the TNF? antagonist administered alone.

Abstract: Described herein are copolymers, and methods of making and utilizing such copolymers. Such copolymers have at least two blocks: a first block that has at least one unit that is hydrophilic at physiologic pH, and a second block that has hydrophobic groups. This second block further has at least one unit with a group that is anionic at about physiologic pH. The described copolymers are disruptive of a cellular membrane, including an extracellular membrane, an intracellular membrane, a vesicle, an organelle, an endosome, a liposome, or a red blood cell. Preferably, in certain instances, the copolymer disrupts the membrane and enters the intracellular environment. In specific examples, the copolymer is endosomolytic.

Abstract: Provided herein are methods directed to the prediction and early assessment of the efficacy of cancer treatment regimens, in particular in patients undergoing therapy with a DNA-damaging chemotherapeutic agent, by determining expression levels of certain proteins found to be useful as biomarkers in circulating tumor cells obtained from the patient both prior to and post-treatment.

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

Abstract: The present invention provides an antibody capable of specifically recognizing and detecting the highly specific cancer marker with respect to the epithelial ovarian cancer, or a fragment of the antibody. The present invention provides an anti-?1,3-N-acetylglucosaminyltransferase 3 antibody for diagnosis of epithelial ovarian cancer, i.e., an antibody for detection of a glycosyltransferase ?1,3-N-acetylglucosaminyltransferase 3 as an epithelial ovarian cancer marker. The antibody recognizes, as an epitope, a part of a polypeptide of the enzyme consisting of the amino acid sequence represented by SEQ ID NO: 1.

Abstract: The invention provides a method for predicting the clinical response to a cancer vaccine in a patient having cancer, a method for determining the immune response to a cancer vaccine in a patient having cancer who has been administered a cancer vaccine, a method for determining the long-term survival in a patient having cancer, corresponding kits therefor, as well as methods of for improving the efficacy of a virus-based vaccine.

Abstract: The present inventors have solved the crystal structure of an Escherichia coli bacterial lipocalin polypeptide, which depicts a monomeric protein. Previous crystal structures have been reported, but these appear to he inaccurate, as they predicted, e.g., a dimeric protein. The crystal structure of a bacterial lipocalin provided by the present invention leads to numerous uses. For example, the present invention provides for the design, construction and use of recombinant libraries of diversified bacterial lipocalins resulting from a bacterial lipocalin polypeptide “backbone”.

Abstract: The present invention relates to polyamides capable of inhibiting ARE-, GRE- and ERE-mediated gene regulation in cells. The present invention also relates to polyamides capable of modulating the activity of RNA polymerase II and p53. The invention also relates to methods to treat diseases related to ARE-, GRE- and ERE-mediated gene regulation and to RNA polymerase II and p53 activity.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Dystrophin family, in particular, by targeting natural antisense polynucleotides of Dystrophin family. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of DMD family.

Abstract: The present invention provides methods, kits, and compositions for producing single-stranded circular DNA by PCR. In particular, hairpin primers are provided, and methods of use thereof to produce single-stranded circular DNA molecules.

Abstract: It is intended to provide a system of predicting the postoperative prognosis in a patient with breast cancer from the viewpoint of gene expression based on the data obtained by genome-wide and comprehensive analysis on gene expression in breast cancer. Expression of human genes is comprehensively analyzed by using a DNA microarray and gene expression functions in various breast cancer conditions are compared, thereby establishing a system of predicting the postoperative prognosis of breast cancer.

Abstract: Genetically modified mice are provided that express human ? variable (hV?) sequences, including mice that express hV? sequences from an endogenous mouse ? light chain locus, mice that express hV? sequences from an endogenous mouse ? light chain locus, and mice that express hV? sequences from a transgene or an episome wherein the hV? sequence is linked to a mouse constant sequence. Mice are provided that are a source of somatically mutated human ? variable sequences useful for making antigen-binding proteins. Compositions and methods for making antigen-binding proteins that comprise human ? variable sequences, including human antibodies, are provided.

Abstract: Processes and C/D box small nucleolar RNAs (snoRNAs) for altering telomerase activity and altering telomerase length are described. The processes of the invention involve the use of C/D box snoRNAs for targeted 2?-O-methylation modification of nucleotides in a pseudoknot region of the telomerase RNA. Depending on their position, the 2?-O-methylation modifications can cause an increase in telomerase activity and subsequent telomere lengthening or a decrease in telomerase activity and subsequent telomere shortening.

Abstract: Methods for affecting mRNA expression or translation through the modification of pre-mRNA or mRNA transcripts are described. In one embodiment of the methods of the present invention, the branch point adenosine of a pre-mRNA transcript is 2?-0-methylated to block splicing and subsequent expression of the protein encoded by the transcript. In another embodiment, a uridine residue in a nonsense stop codon may be modified to pseudouridine, causing the translation machinery to read through the nonsense stop codon and translate a full length protein.

Abstract: Disclosed is a simple and highly efficient method for introducing a gene into a target cell using a retrovirus vector. The method comprises the steps of (a) placing a liquor containing a retrovirus vector having a foreign gene carried thereon into a bag for cell culture on which a retrovirus-binding substance has been immobilized, and incubating the liquor at a temperature lower than 25° C. for 8-48 hours, thereby producing a culture bag having the retrovirus vector bound thereto, (b) adding a target cell to the culture bag that has been produced in step (a) and incubating the culture bag for 8 hours or less, and (c) flipping the culture bag upside down and incubating the culture bag. The gene introduction method is useful particularly in medicine, cell technology, gene technology, and embryologic technology.