Abstract: The present invention discloses a process for engineering a host cell comprising the steps of; a) integrating a first polynucleotide cassette including a first selection marker flanked by a first pair of recombination sites; b) removing the first selection marker by the action of a recombinase which recognises the first pair of recombination sites; c) integrating a second polynucleotide cassette including a second selection marker flanked by a second pair of recombination sites; and d) removing the second selection marker by the action of a recombinase which recognises the second pair of recombination sites. Also disclosed is a host cell genome polynucleotide comprising a first recombinantly engineered region and a second recombinantly engineered region, wherein a first single recombination site is adjacent to the first recombinantly engineered region, and a second single recombination site is adjacent to the second recombinantly engineered region.

Abstract: The present disclosure provides compositions and methods for enhanced expression of exogenous genes in eukaryotic cells. The method involves introducing into a mammalian cell an exogenous nucleic acid. wherein the exogenous nucleic acid intearates into a locus of the genome that comprises an extended methylation-free CpG island. Also provided are chromosomal loci, sequences for enhanced and stable expression of exogenous genes.

Abstract: Disclosed herein are homology-independent targeted integration methods of integrating an exogenous DNA sequence into a genome of a non-dividing cell and compositions for such methods. Methods herein comprise contacting the non-dividing cell with a composition comprising a targeting construct comprising the exogenous DNA sequence and a targeting sequence, a complementary strand oligonucleotide homologous to the targeting sequence, and a nuclease, thereby altering the genome of the non-dividing cell.

Abstract: An extrudable hydrogel composition useful for making a three-dimensional organ construct is described herein. Methods of using the same and products so made are also described. Also described herein is a multicellular organoid including at least two tumor cells or cell lines that are of the same tissue type, but are distinct from one another (e.g., distinct in morphology, growth rate, and/or at least one mutation); and at least one type of non-cancerous (i.e., normal or differentiated) tissue cells, wherein the at least one type of non-cancerous tissue cells are of the same tissue type as the at least two tumor cells or cell lines. In some embodiments, the at least two tumor cells or cell lines and/or the non-cancerous tissue cells are labeled with and/or comprise a detectable compound, optionally so that each of the different cells can be distinguished from each other (e.g., optically and/or electrically distinguished).

Abstract: Provided herein are methods of reducing or eliminating undifferentiated pluripotent stem cells, where the methods comprise contacting an effective amount of a compound to a heterogeneous cell population or sample comprising or suspected of comprising differentiated cell types and undifferentiated pluripotent stem cells, whereby the contacting selectively reduces or eliminates undifferentiated pluripotent stem cells from the cell population or sample. Also provided are methods for obtaining a population of stem cell-derived cell types substantially free of undifferentiated pluripotent stem cells as well as isolated populations of such of stem cell-derived cell types.

Abstract: Methods of generating a synthetic embryo are provided. Accordingly, there is provided a method of generating a synthetic embryo comprising inducing expression of a factor that induces differentiation to trophectoderm cells in a subpopulation of naïve pluripotent stem cells (PSCs) to obtain a trophectoderm primed cells; inducing expression of a factor that induces differentiation to extra embryonic primitive endodermal cells in a second subpopulation of naïve PSCs to obtain extra embryonic primitive endodermal primed cells; and mixing said trophectoderm primed cells and said extra embryonic primitive endodermal primed cells with naïve PSCs under conditions that allow formation of aggregated cells. Also provided are articles of manufactures, mixtures and aggregates of cells and methods of using same.

Abstract: Provided is an isolated population of human pluripotent stem cells comprising at least 50% human pluripotent stem cells characterized by an OCT4+/TRA1-60?/TRA1-81?/SSEA1+/SSEA4? expression signature, and novel methods of generating and maintaining same in a pluripotent, undifferentiated state a suspension culture devoid of cell clumps. Also provided are novel culture media, cell cultures and methods for culturing pluripotent stem cells in a suspension culture or a two-dimensional culture system while maintaining the cells in a proliferative, pluripotent and undifferentiated state. The novel culture media comprise interleukin 11 (IL11) and Ciliay Neurotrophic Factor (CNTF); bFGF at a concentration of at least 50 ng/ml and an IL6RIL6 chimera; or an animal contaminant-free serum replacement and an IL6RIL6 chimera. Also provided are methods for generating lineage-specific cells from the pluripotent stem cells.

Abstract: A method of altering cells comprising culturing them in a growth factor gradient, wherein said gradient is provided by a polyhedra delivery system (PODS) that releases the growth factor to set up the gradient.

Abstract: As a technique for proliferating neural crest cells without reducing differentiation capacity, provided is a method for producing neural crest cells, comprising the steps of: (1) obtaining neural crest cells; and (2) suspension-culturing the neural crest cells in a medium comprising a GSK3? inhibitor and a basic fibroblast growth factor (bFGF), wherein the medium comprises the GSK3? inhibitor with a concentration that exhibits an effect equivalent to that exhibited by CHIR99021 with a concentration of higher than 1 ?M and lower than 5 ?M.

Abstract: A cell activation reactor and a cell activation method are provided. The cell activation reactor includes a body, a rotating part, an upper cover, a microporous film, and multiple baffles. The body has an accommodating space, which is suitable for accommodating multiple cells and multiple magnetic beads. The rotating part is disposed in the accommodating space and includes multiple impellers. The microporous film is disposed in the accommodating space and covers multiple holes of the accommodating space. The baffles are disposed in the body. When the rotating part is driven to rotate, the interaction between the baffles and the impellers separates the cells and the magnetic beads.

Abstract: Embodiments of the disclosure include methods and compositions for use of prepared fibroblasts and/or conditioned media therefrom. In particular embodiments, the prepared fibroblasts have enhanced regenerative and may have an increase in secretion of one or more cytokines and/or growth factors; may have an increase in anti-apoptotic activity; and/or may have a modulated immunogenicity. In specific embodiments, the fibroblasts are prepared by exposure to hypoxia and/or carbon monoxide.

Abstract: Provided is a method for inducing pluripotent stem cells to differentiate into somatic cells in a culture medium containing a heparin binding growth factor, the method comprising bringing cells into contact with a conjugate of a laminin E8 fragment and a growth factor binding domain-containing fragment of a heparan sulfate proteoglycan. According to the present invention, pluripotent stem cells can be induced to differentiate into any desired somatic cells in a highly efficient manner.

Abstract: The presently disclosed subject matter provides for in vitro methods of inducing differentiation of human stem cells into neural crest, cranial placode or non-neuro ectoderm precursors, and cells generated by such methods. The presently disclosed subject matter also provides for uses of such cells for treating neurodegenerative and pituitary disorders.

Abstract: Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.

Abstract: The present invention relates to compositions, methods and use of a mixture of enzymes having DNase activity and an enzyme having hexosaminidase activity.

Abstract: The present invention relates to variants of an alpha-amylase having improved stability to chelating agents relative to its parent enzyme, compositions comprising the variants, nucleic acids encoding the variants, methods of producing the variants, and methods for using the variants.

Abstract: The present invention provides engineered protease polypeptides and compositions thereof. The engineered protease polypeptides have been optimized to provide improved activity, improved thermostability, protease stability, autolytic stability, and stability under a range of pH conditions, including acidic (pH<7) and basic (pH>7) conditions. The invention also relates to the use of the compositions comprising the engineered protease polypeptides for therapeutic and/or nutritional purposes. The present invention also provides polynucleotides encoding the engineered protease polypeptides, as well as methods for making the engineered polynucleotides and protease polypeptides.

Abstract: A horseshoe crab Factor C protein having activity of Factor C, wherein the horseshoe crab is selected from Tachypleus tridentatus, Limulus polyphemus, and Carcinoscorpius rotundicauda, and wherein the horseshoe crab Factor C protein is produced through being recombinantly expressed from a Chinese Hamster Ovary (CHO) DG44 cell or HEK cell.

Abstract: During the process of coagulation, prothrombin is activated to ?-thrombin by prothrombinase. Key residues in the structure of prothrombin allow for modulation of the activation of prothrombin. In certain embodiments, a recombinant prothrombin with at least one point mutation or deletion is provided.

Abstract: The present invention relates to cleaning compositions comprising polypeptides having peptidoglycan degradation activity, as well as use of the cleaning compositions for cleaning of an item such as a textile or a surface.

Abstract: Cotton-containing textiles, such as “trash” feedstock in terms of end-of-life-cotton textiles, may be used to produce sugar without the same kinds of harsh pretreatments used for other biomasses, such as corn, grass sources, or wood. Disclosed is a process for production of sugar from a cotton-containing textile waste fabric comprising optionally mechanically pretreating the cotton-containing textile, pretreating the cotton-containing textile with an acid pretreatment to form a slurry, cooling the slurry, adding at least one base to the slurry, adding at least one additional acid to the slurry to form a buffer in situ, adding a hydrolysis enzyme, and optionally filtering the slurry.

Abstract: The disclosure discloses a production process and application of fermented tapioca starch for baking, and belongs to the fields of starch deep processing and food processing and production. The disclosure develops a production method of the fermented tapioca starch for baking. The method includes simple steps and greatly shortens a process cycle. By using tapioca starch as a main raw material and adding a specific amount of carbon source and a specific strain, under the action of fermentation and illumination in cooperation, the structure of the starch is improved. By adding the fermented tapioca starch, the effects of increasing the size of gluten-free Mochi bread, increasing pores of the bread and improving the texture and taste of the bread are realized.

Abstract: Embodiments of the present disclosure relate to materials and methods for preparing a clathrate-forming composition comprising a plurality of linear glucomonomer chains of about 15 to about 100 D-glucopyranosyl residues linked by ?-1,4 linkages, wherein the linear glucomonomer chains are a product of partial amylolysis of a modified starch substrate and wherein the product is flowable at temperatures within a range of 4-20° C. at about 20% w/v solids content. The present disclosure further describes methods of using the clathrate-forming compositions to form molecular dispersions or clathrates with hydrophobic guest molecules, kits for use in these methods, and molecular dispersions or clathrates obtained from the materials.

Abstract: A saccharification reaction mixture can saccharify at least one of cellulose and hemicellulose and contains at least one of cellulose and hemicellulose, a saccharification enzyme, silica or a silica-containing substance, and at least one compound (A) selected from the group consisting of a polyhydric alcohol compound represented by the following formula (1) or a derivative thereof and an acetylene glycol represented by formula (2) or an alkylene oxide adduct thereof.

Abstract: The present invention addresses the problem of providing a method for producing nicotinamide mononucleotide, that produces nicotinamide mononucleotide using a single enzyme and using nucleoside monophosphate, pyrophosphate, and nicotinamide as starting materials. This problem is solved by a nicotinamide mononucleotide production method that includes at least the following steps 1) and 2): 1) a first step of producing phosphoribosyl diphosphate by the action of substantially one enzyme on nucleoside monophosphate and pyrophosphate; and 2) a second step of producing nicotinamide mononucleotide by the action of only substantially the aforementioned one enzyme on nicotinamide and the phosphoribosyl diphosphate that is the product of the first step.

Abstract: The present invention includes novel systems, methods, and compositions for the enzymatic/chemical production of pseudouridine (?) and its variants, such as N1-methyl-pseudouridine-5?-triphosphate (m1?TP).

Abstract: The present invention is directed to methods and compositions for the production of Fc-containing polypeptides having improved properties and comprising mutations at positions 243 and 264 of the Fc region.

Abstract: Systems and methods that include starch derived from grain as a carbon source for propagation of microorganisms.

Abstract: Provided herein are methods of producing oils with reduced saturated fatty acids. The methods include culturing oil-producing microorganisms in a fermentation medium in the presence of one or more antifoaming agents under a controlled carbon consumption rate, wherein the culturing produces oils comprising fatty acids and wherein less than 35% of the fatty acids in the oil are saturated fatty acids.

Abstract: The invention relates to the detection of the cofactor reduced nicotinamide adenine dinucleotide phosphate (NADPH). Provided is a sensor molecule for the resonance energy transfer (RET)-based detection of NADPH, the sensor comprising a segment A connected via a linker to a segment B, wherein each of segment A and segment B comprises a member of a RET pair comprising a donor moiety and an acceptor moiety, further characterized in that (i) segment A comprises a binding protein (BP) for NADPH, the BP being dihydrofolate reductase (DHFR; EC 1.5.1.3) or a functional homolog, fragment, derivative or variant thereof, showing the desired NADPH binding properties, and wherein the BP comprises a heterologous protein domain inserted at or replacing at least part of the region corresponding to positions (20) to (27) of E.

Abstract: A method for assessing microbial drug resistance multi-level risks of antibiotic residues in water environments, belonging to the technical field of water environment assessment, comprises the following steps: S1, environment monitoring; S2, preliminary screening of antibiotics: S2-1, determination of n-octanol/water partition coefficient, and S2-2, determination of antibiotic environment concentration; S3, assessment of microbial drug resistance; and S4, high-level assessment. The assessment method of the present disclosure conducts a step-by-step assessment of target antibiotics or target antibiotic derivatives in water environment with risks.

Abstract: The present invention aims to provide a novel method that can quantify diaminopimelic acid-containing bacteria in a test sample. The present invention relates to a method of quantifying diaminopimelic acid-containing bacteria in a test sample, including a step of quantifying the diaminopimelic acid-containing bacteria, using, as an index, the amount of diaminopimelic acid derived from the diaminopimelic acid-containing bacteria in the test sample.

Abstract: Disclosed are methods and systems for the analysis activity of enzyme disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13 (ADAMTS13) in a sample. The methods and systems disclosed herein can be useful for diagnosis of thrombotic thrombocytopenic purpura in a patient.

Abstract: Disclosed herein are methods of extracting genetic material from a diverse population of one or more types of microbes in a sample. Microbes can be prokaryotes or eukaryotes and may include bacteria, archaea, fungi, protozoa, helminths, parasites, viruses, phages, and others. Extraction may be from a single sample and subsequent identification may be through a molecular method such as qPCR, PCR, RFLP, SSCP, allele specific PCR, targeted sequencing, pull down sequencing, whole shotgun sequencing, or other methods. Also provided are methods that include extracting nucleic acid molecules from a variety of organisms such as fungi (i.e., Saccharomyces spp.), animal cells (Bos taurus), plants (e.g., Hordeum vulgare) from the gut of a human subject, performing a metagenomics analysis therefrom, and determining a probiotic treatment or dietary guidance for the subject based on the metagenomics analysis.

Abstract: The present technology provides for an apparatus for detecting polynucleotides in samples, particularly from biological samples. The technology more particularly relates to microfluidic systems that carry out PCR on nucleotides of interest within microfluidic channels, and detect those nucleotides. The apparatus includes a microfluidic cartridge that is configured to accept a plurality of samples, and which can carry out PCR on each sample individually, or a group of, or all of the plurality of samples simultaneously.

Abstract: Temperature sensitive transcriptional bioswitches and related genetic circuits and in particular bandpass and/or multiplex genetic circuits, vectors, cells, compositions methods and systems are described.

Abstract: The present invention relates to the field of noninvasive prenatal gene testing by high-through sequencing technologies. Particularly, the present application relates to a method for determining the content of cell-free fetal DNA in maternal peripheral blood.

Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Abstract: The present invention relates to a method for measuring a mutation rate, comprising preparing a library for next generation sequencing (NGS). Accordingly, the present invention can measure the effect of drugs, radiation, gene composition, aging, and various stresses experienced by an individual, etc. on the occurrence of mutations in a subject sample, and thus can be used for testing, diagnosis, management and evaluation related to toxicity tests, medical tests, maintenance and management of health, etc.

Abstract: Methods and devices are provided for simultaneously amplifying a plurality of sample wells for a predetermined amount of amplification, detecting whether amplification has occurred in a first set of the wells, amplifying for an additional amount of amplification and detecting whether amplification has occurred in a second set of the wells. Methods are also provided for analyzing a target nucleic acid sequence using melt curves that were generated in a plurality of amplification cycles.

Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.

Abstract: Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.

Abstract: The invention relates to a new method of determining the presence, absence or characteristics of an analyte. The analyte is coupled to a membrane. The invention also relates to nucleic acid sequencing.

Abstract: This disclosure provides methods for bisulfite-free identification in a nucleic acid sequence of the locations of 5-methylcytosine, 5-hydroxymethylcytosine, 5-carboxylcytosine and 5-formylcytosine.

Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.

Abstract: Embodiments of the present disclosure relate to nucleotides labeled with photoswitchable compounds. Also provided herein are methods and kits of using these labeled nucleotides for sequencing applications.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: A method for evaluating or monitoring metabolic effects of exercise or injury by detecting and/or quantifying microR-NAs in saliva. Compositions and methods of treatment based on detection of microRNAs.

Abstract: Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.