Abstract: The present application provides a group of human immortalized B lymphocyte cell lines and use thereof, and specifically provides a combination of four closely related immortalized lymphocyte cell lines. The combination can be used as a reference substances for measuring the performance of a detection platform. When the four closely related immortalized lymphocyte cell lines are used as reference substances for epigenome, transcriptome, proteome, and metabolome, an intrinsic magnitude difference gradient can be formed to evaluate the sensitivity of histological detection.

Abstract: Provided are a method for producing stem cell-derived extracellular vesicles by using a three-dimensional cell culture process, use of three-dimensional cell aggregates of stem cells in producing extracellular vesicles, a culture of three-dimensional cell aggregates of stem cells comprising a high concentration of extracellular vesicles, and a pharmaceutical composition comprising the culture.

Abstract: Some embodiments are directed to a method for preparing a skin substitute, a dermal substitute, to a skin substitute, to a dermal substitute and to a kit for implementing the method. Some other embodiments are directed to a graft that can consist of of a skin substitute and to the use thereof as treating a skin disorder and/or a loss of skin substance.

Abstract: Certain embodiments are directed to an improved RVF vaccine for human use, and method for producing the same.

Abstract: A method and composition for inactivating both naked genetic material such as RNA and DNA and inactivating mechanical delivery vectors in a treatment space external of the human body. To practice the method, apply a mist of lipid molecule degrading agent effective against viral membranes with lipid molecules. Then apply an inactivator of spike proteins and other viral residues. Next, reduce the threat of transmitting genetic material by applying inactivators of mechanical transport vectors such as mold, yeast, and bacteria. Further, pretreat the treating space to receive enzymatic agents by applying a surface detoxifying agent in quantity sufficient to inactivate substances detrimental to enzymes that break the naked viral genetic material. Then, apply preparatory enzymes that degrade microorganisms and their cellular components. Finally, apply enzymes for breaking the naked viral genetic material, as present.

Abstract: The present invention provides engineered penicillin G acylase (PGA) enzymes, polynucleotides encoding the enzymes, compositions comprising the enzymes, and methods of using the engineered PGA enzymes.

Abstract: The present invention pertains to a novel architecture of non-ribosomal peptide synthases (NRPS). The invention provides artificial NRPS wherein the naturally occurring terminal condensation or thioesterase-domain is replaced by internal condensation or dual condensation/epimerization domains. Moreover, the present invention enables the portability of terminal condensation domains to unrelated NRPS in respect of peptide release of linear peptides. The replacement results in a product independent release of the synthesized product and therefore enables the rational design of NRPS. The invention provides the new NRPS, nucleic acids encoding them, methods for artificial NRPS generation, and methods for producing non-ribosomal peptides.

Abstract: An incubator-actuator device including a sample chamber, a magnetic field generating coil, and a light-emitting diode (LED) placement cage is provided herein. The incubator-actuator device is configured for simultaneous optical irradiation and oscillating magnetic field irradiation of a mammalian cell or a nanostructure. A system including an incubator-actuator device including a sample chamber, a magnetic field generating coil, and a light-emitting diode (LED) placement cage, and a laser is also provided herein. The system is configured for simultaneous optical irradiation and oscillating magnetic field irradiation of a target.

Abstract: One aspect of the present invention provides a nucleic acid extraction device. The nucleic acid extraction device includes a container which stores each of a cleaning solution and an eluting solution, a water level sensor configured to detect amounts of the cleaning solution and the eluting solution which are stored in the container, a tube sensor configured to sense a sample tube disposed on a sample tube accommodation portion, and an operation initiation portion configured to determine whether the cleaning solution and the eluting solution which are necessary for a nucleic acid extraction operation are provided on the basis of the number of such sample tubes which is sensed by the tube sensor and the amounts of the cleaning solution and the eluting solution which are sensed by the water level sensor.

Abstract: The present invention provides a method and a system for the isolation and purification of nucleic acids from nucleic acid-containing material using a modified porous material containing cationic groups in a solid-liquid phase system. In some embodiments, the present invention is capable of obtaining nucleic acids with sufficient purity and quantity in a relatively simple way to enable accurate subsequent analysis or processing. In some embodiments, the liquid phase comprises an aqueous two-phase system (ATPS), comprising a first phase and a second phase, and the solid phase comprises a porous material, wherein the two phases travel through the porous material. In some embodiments, the nucleic acids enter the pores of the porous material and subsequently travel through the porous material while preferentially partitioning into one of the phases.

Abstract: A system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The symbol library has a number of DNA symbols each having a first overhanging end and a second overhanging end different than and non-complimentary to the first end, the first and second ends being the same nucleotides for each DNA symbol. The linker library has pairs of DNA linkers, a first linker of a pair having a first end and a second end and a second linker of the pair having a first end and a second end, the first end of the first linker being the same nucleotides for each first linker and the second end of the second linker being the same nucleotides for each second linker, wherein the second end of the first linker and the first end of the second linker have complementary nucleotides. The first linker joins to the first end of a DNA symbol and the second linker joins to the second end of another DNA symbol.

Abstract: The present invention addresses the problem of providing a novel method which is for preparing a DNA fragment for microbial cell transformation, and by which the combinatorial library of a long-chain DNA can be efficiently constructed and confirmation of the genotype of the obtained clone is facilitated.

Abstract: The present disclosure provides a method for screening cells, the method including a step of preparing a plurality of cells which are tagged with a first barcode nucleic acid associated with a test target and treated with the test target, a step of sorting the plurality of cells based on cellular phenotype using an imaging cell sorter, and a step of identifying the test target used to treat each cell using the first barcode nucleic acid as an indicator.

Abstract: The invention provides, inter alia, methods for uniquely labeling populations of agents of interest using random combinations of oligonucleotides. The oligonucleotides may comprise a unique nucleotide sequence and/or one or more non-nucleic acid detectable moieties.

Abstract: The present invention provides a method of selecting a mRNA for production of a polypeptide of interest comprising: a) producing an array of individual mRNA sequences comprising different nucleotide sequences encoding the polypeptide of interest; b) determining one or more or two or more of the following parameters for each individual mRNA sequence of (a): (i) minimum free energy (MFE) RNA secondary structure; (ii) ensemble free energy (EFE); (iii) frequency of the minimum free energy (FMFE) RNA secondary structure in a thermodynamic ensemble; and (iv) ensemble diversity (ED); c) ranking the individual mRNA sequences of the array according the parameters determined in step (b); and d) selecting a mRNA sequence from the ranked array of step (c), wherein the selected mRNA produces the polypeptide of interest. The present invention further provides a method of selecting a mRNA for enhanced and reduced production of a polypeptide of interest.

Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

Abstract: The invention provides methods for treating or preventing microbial (eg, bacterial) infections and means for performing these methods. In particular, treatment of infections requiring rapid and durable therapy is made possible, such as for treating acute conditions such as septicemia, sepsis, SIRS or septic shock. The invention is particularly useful, for example, for treatment of microbes such as for environmental, food and beverage use. The invention relates inter alia to methods of controlling microbiologically influenced corrosion (MIC) or biofouling of a substrate or fluid in an industrial or domestic system. The invention also useful for the treatment of pathogenic bacterial infections in subjects receiving a treatment for a disease or condition, such as a transplant or a treatment for cancer, a viral infection or an autoimmune disease.

Abstract: The disclosure describes novel systems, methods, and compositions for the manipulation of nucleic acids in a targeted fashion. The disclosure describes non-naturally occurring, engineered CRISPR-Cas systems, components, and methods for targeted modification of nucleic acids such as DNA. Each system includes one or more protein components and one or more nucleic acid components that together target nucleic acids.

Abstract: Disclosed herein are methods and compositions for enhancing gene targeting. The method entails co-administrating to a cell a targeting molecule and a means of enhancing the function of the targeting molecule upon delivery to the cell. The means of enhancing the function of the targeting molecule including one or more of a stressor that induces cellular stress, a proton sponge molecule, and an endosome or lysosome inhibitor. Compositions disclosed include a targeting molecule and one or more of a stressor that induces cellular stress, a proton sponge molecule, and an endosome or lysosome inhibitor.

Abstract: The present invention provides methods for cancers associated with a TERT promoter mutation in a subject. In some embodiments, the methods comprise administering to the subject a therapeutically effective amount of an agent that specifically reduces or inhibits GA binding protein transcription factor beta subunit 1 long isoform (GABPBIL) expression or function.

Abstract: The present invention relates to chirally controlled oligonucleotides, chirally controlled oligonucleotide compositions, and the method of making and using the same. The invention specifically encompasses the identification of the source of certain problems with prior methodologies for preparing chiral oligonucleotides, including problems that prohibit preparation of fully chirally controlled compositions, particularly compositions comprising a plurality of oligonucleotide types. In some embodiments, the present invention provides chirally controlled oligonucleotide compositions. In some embodiments, the present invention provides methods of making chirally controlled oligonucleotides and chirally controlled oligonucleotide compositions.

Abstract: Provided is a short-chain guide RNA that is able to induce site-specific editing even when only a small number of nucleotides is attached to the target recognition site. The guide RNA includes a first oligonucleotide that identifies the target RNA, and a second oligonucleotide that links to the 3? end of the first oligonucleotide. The first oligonucleotide contains: a target-corresponding nucleotide residue that corresponds to an adenosine residue in the target RNA; an oligonucleotide of 15 to 30 residues that links to the 5? end of the target-corresponding nucleotide residue and that has a base sequence complementary to the target RNA; and an oligonucleotide of 3 or 4 residues that links to the 3? end of the target-corresponding nucleotide residue and that has a base sequence complementary to the target RNA. The second oligonucleotide contains 2 to 24 nucleotide residues, and induces site-specific editing of the target RNA.

Abstract: Disclosed herein are conditional siRNAs activatable by CBF?-MYH11 oncogenic gene and use thereof for treating conditions such as acute myeloid leukemia (AML). The conditional siRNAs target MCL-1 or HDAC8.

Abstract: The present invention provides a novel nucleoside derivative or a salt thereof, a polynucleotide synthesis reagent, a method for producing a polynucleotide, a polynucleotide, and a method for producing a binding nucleic acid molecule. The nucleoside derivative or a salt thereof of the present invention is represented by the following chemical formula (1). In the chemical formula (1), Su is an atomic group having a sugar skeleton at a nucleoside residue or an atomic group having a sugar phosphate skeleton at a nucleotide residue, and may or may not have a protecting group, L1 and L2 are each independently a straight-chain or branched, saturated or unsaturated hydrocarbon group having 2 to 10 carbon atoms, X1 is an imino group (—NR1—), an ether group (—O—), or a thioether group (—S—), and R1 is a hydrogen atom or a straight-chain or branched, saturated or unsaturated hydrocarbon group having 2 to 10 carbon atoms.

Abstract: The present invention is directed to an aptamer composition comprising at least one oligonucleotide consisting of: deoxyribonucleotides, ribonucleotides, derivatives of deoxyribonucleotides, derivatives of ribonucleotides, and mixtures thereof; wherein said aptamer composition has a binding affinity for one or more bacterial species from the genera Prevotella and Porphyromonas.

Abstract: This disclosure relates to targeted protease compositions and uses related thereto. In certain embodiments, the disclosure relates to nanoparticles wherein a targeting molecule is linked to the nanoparticle and wherein a catalytic domain of a protease is linked to the nanoparticle. In certain embodiments, the targeting molecule and the catalytic domain are within a single polypeptide sequence. In certain embodiments, the targeting molecule binds a molecule more highly expressed on cancer cells then non-cancerous cells, and the nanoparticles disclosed herein are used for the treatment of cancer by further attaching an anti-cancer agent to the nanoparticle or incorporating an anticancer agent within the nanoparticle.

Abstract: The invention relates to the ADH3 promoter; polynucleotide sequences, vectors and expression cassettes including DNA regions responsible for the regulation of the ADH3 promoter; the host cells, including these vectors and expression cassettes, and, the recombinant proteins performed with the developed cells. In the scope of the invention, deletion analyzes in the ADH3 promoter were performed to identify regions that affect promoter strength and significant data was obtained in the formation of mutant ADH3 promoters. Deletion of the nucleotides between 539 and 638 (?361 to ?262) in SEQ ID NO: 1 resulted in a 63% increase in ADH3 promoter activity. Five different synthetic promoters were created using positive regulatory regions identified and approximately 165% to 200% promoter activities were achieved with these promoters.

Abstract: The present invention relates to methods and compositions for modifying a target site in the genome of a plant cell. Such modifications include integration of a transgene and mutations. The present invention also relates to methods and compositions for identifying and enriching for cells which comprise a modified target site.

Abstract: Methods and compositions for modulating shoot apical meristem size are provided. Methods are provided for modulating the expression of fea3 sequence in a host plant or plant cell to modulate agronomic characteristics such as altered size and number of organs, including plant seeds.

Abstract: The present invention relates to a cell line, use of the cell line and a method for producing infectious viral particles using said cell line.

Abstract: An intracellular delivery system and method are provided. The intracellular delivery system comprises a laser-activated surface and cells positioned at a distance from the laser-activated surface. A laser provided a laser pulse that is used to porate membranes of the cells to deliver or extract cargo from the cells into a liquid surrounding the cells. The method of intracellular delivery comprises positioning a laser-activated surface at a distance from cells and applying a laser pulse from the laser to the surface to porate membranes of the cells to deliver or extract cargo from the cells into a liquid surrounding the cells.

Abstract: Provided herein are CRISPR/Cas9 complexes and method of using same.

Abstract: The present invention relates to systems and methods for recording and assaying cellular events, in particular gene expression. The invention provides hereto a method of determining a cellular event of interest in a cell comprising providing a cell comprising a CRISPR-Cas system, wherein the CRISPR-Cas system comprises a guide RNA that targets a selected DNA sequence and a Cas protein capable of modifying the selected DNA sequence; whereby a nucleic acid molecule encoding at least one of the guide RNA or Cas protein is operably connected in the cell with a regulatory element comprising a promoter responsive to the cellular event, and whereby expression of at least one CRISPR-Cas system component is driven by the promoter; and determining cellular event of interest based on detection of the modification of the selected DNA sequence.

Abstract: Described herein are methods of enhancing chromosomal homologous recombination to stimulate a loss of heterozygosity at a gene locus of interest in a living cell. These methods are driven by an enhancer component and a target-specific endonuclease component and proceed through a mechanism whereby: exogenous donor DNA that is homologous to the gene locus of interest is not introduced into the living cell; the desired allele of the gene locus of interest remains uncleaved; and the undesired allele is either uncleaved, cleaved at a single location, or cleaved at multiple locations. These methods have numerous applications, including the repair of risk alleles for disease prevention, the correction of heterozygous mutations in dividing cells, the design of cancer therapeutics, and the design of novel gene-drive strategies.

Abstract: Described herein are systems and methods for treating, inhibiting, or ameliorating X-linked disorders including Wiskott-Aldrich Syndrome (WAS) and X-linked thrombocytopenia (XLT) in subjects that have been identified or selected as being ones that would benefit from a therapy to treat, inhibit, or ameliorate WAS or XLT. The systems include nuclease and vector donor constructs configured for co-delivery to modify endogenous WAS locus.

Abstract: The invention pertains to an inducible CRISPR system for controlling expression of a CRISPR complex with an inducible fusion promoter. One embodiment of the invention provides HIV LTR-minimal Drosophila hsp70 fusion promoter that can be used for inducible co-expression of gRNA and Cas9 in HIV-infected cells to target cellular cofactors such as Cyclin T1. A single introduction of such embodiment leads to sustained suppression of HIV replication in stringent, chronically infected HeLa-CD4 cell lines as well as in T-cell lines. In another embodiment, the invention further relates to enhancement of HIV suppression by incorporating cis-acting ribozymes immediately upstream of the gRNA in the inducible CRISPR system construct. The inducible fusion promoter is adaptable for other tissue- or cell-type specific expression of the inducible CRISPR system.

Abstract: Provided is a process for synthesizing a functionalized cyclic dithiocarbamate.

Abstract: Disclosed are methods for the pre-treatment of lignocellulose by adding an alkali or acid reagent(s) during the densification thereof, and for the biotransformation thereof. In the method, an alkali reagent(s) or acid reagent(s) is added to a lignocellulosic raw material for a densification pre-treatment to form an alkali- or acid-containing densified lignocellulose with a compressed compact shape, thereby achieving the pre-treatment. The acid or alkali in the pre-treated lignocellulose can further pre-treat the lignocellulosic raw material in a mild manner during the subsequent transportation and storage processes. If a subsequent pre-treatment is needed, then the severity thereof is reduced substantially; in addition, the uniform mixing of the acid or alkali with the lignocellulose and a large density of the raw material promote a high efficiency and a high loading capacity of the subsequent pre-treatment of the densified lignocellulose. The method is simple and efficient.

Abstract: The invention provides compositions and methods for engineering E. coli or other host production bacterial strains to produce fucosylated oligosaccharides, and the use thereof in the prevention or treatment of infection.

Abstract: The present invention is broadly concerned with new in vitro glycosylation methods that provide rational approaches for producing glycosylated proteins, and the use of glycosylated proteins. In more detail, the present invention comprises methods of glycosylating a starting protein having an amino sidechain with a nucleophilic moiety, comprising the step of reacting the protein with a carbohydrate having an oxazoline moiety on the reducing end thereof, to covalently bond the amino sidechain of the starting protein with the oxazoline moiety, wherein the glycosylated protein substantially retains the structure and function of the starting protein. Target proteins include oxidase, oxidoreductase and dehydrogenase enzymes. The glycosylated proteins advantageously have molecular weights of at least about 7500 Daltons. In a further embodiment, the present invention concerns the use of glycosylated proteins, fabricated by the methods disclosed herein, in the assembly of amperometric biosensors.

Abstract: The invention features devices and kits for capturing and culturing microorganisms (e.g., bacteria, fungi, or protists) and methods of using the devices and kits to detect microorganisms in environmental and other samples. The device includes a nutrient media having a flat growth area on which microorganisms can grow. Samples are collected by contacting the device with any environmental sample, e.g., rolling device on a work surface or exposing device to air, or by filtering a sample through a membrane. Microorganisms deposited on the membrane derive nutrients from the underlying media and grow into colonies that can then be detected using methods known in the art. The detected colonies can be imaged digitally or with film.

Abstract: A method for analysis of yeast includes: receiving a microscopic image of yeast by a cloud server (2901), the microscopic image including a scaling pattern for determining a magnification; determining the magnification by the cloud server based on the scaling pattern (2902); and analyzing, by the cloud server, the microscopic image based on the magnification to obtain an analysis result (2903).

Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.

Abstract: A workflow for direct qPCR quantification of unprocessed forensic casework samples is disclosed herein. 13 pg of DNA has been detected by direct amplification from a paper substrate. Direct qPCR quantification of unprocessed forensic casework samples and direct STR amplification of unprocessed forensic casework samples collected on the same PE-swab will greatly increase forensic laboratory's efficiency and capability.

Abstract: Apparatus, systems, chips, and methods of performing a large number of simultaneous chemical reactions are provided herein. The chips of the invention comprise addressable units that can be addressed according to the temperature of the reaction to be run. The subject apparatus, systems, and chips are particularly suited for performing polymerase chain reactions on thousands of nucleic acid sequences, up to and including sequences of an entire genuine of an organism of interest.

Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.

Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described method.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.