Abstract: Expression constructs and methods for recombinant parvovirus production are disclosed. In some embodiments, the expression construct encodes (1) adenovirus E4 and E2a proteins, (2) parvovirus proteins necessary for the production of the recombinant parvovirus, and (3) a recombinant parvovirus genome, thus allowing production of the recombinant parvovirus by transfecting a host cell with a single expression construct.

Abstract: A CpG-modified recombinant adeno-associated viral (AAV) vector is described. The vector carries a nucleic acid molecule comprising AAV inverted terminal repeat (ITR) sequences and an exogenous gene sequence under the control of regulatory sequences which control expression of the gene product, in which the nucleic acid sequences carried by the vector are modified to significantly reduce CpG di-nucleotides such that an immune response to the vector is reduced as compared to the unmodified AAV vector. Also provided are methods and regimens for delivering transgenes using these AAV viral vectors, in which the innate immune response to the vector and/or transgene is significantly modulated.

Abstract: The disclosure relates to modified orthopoxvirus vectors, as well as methods of using the same for the treatment of various cancers. The disclosure provides modified orthopoxvirus vectors that exhibit various beneficial therapeutic activities, including enhanced oncolytic activity, spread of infection, immune evasion, tumor persistence, capacity for incorporation of exogenous DNA sequences and safety. The viruses we have discovered are also amenable to large scale manufacturing protocols.

Abstract: Gene therapy for a retinal disease, injury, or condition in a subject involves administering to the subject a pharmaceutical composition containing a recombinant adeno-associated viral vector encoding at least one heat shock protein, such as Hsp27. A recombinant adeno-associated viral vector can include a promoter sequence that induces production of a heat shock protein specifically in retinal ganglion cells. The loss of such cells causes retinal damage and loss of eyesight in patients afflicted with an ocular condition. The disclosed viral vector may be included in pharmaceutical compositions that may be administered intravitreally using an administration device. A single injection 10 may be therapeutically sufficient for treating various ocular conditions.

Abstract: Compositions and methods for efficiently generating and identifying accurate homologous recombination events are disclosed.

Abstract: Systems and methods for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. Novel nucleic acid targeting systems comprise components of CRISPR systems and non-LTR retrotransposon elements.

Abstract: Described herein are engineered nucleases comprising mutations in the cleavage domain (e.g., FokI or homologue thereof) and/or DNA binding domain (zinc finger protein, TALE, single guide RNA) such that on-target specificity is increased.

Abstract: Processes and systems for biologically producing hydrogen gas from organic waste, including food waste. Such a process includes biologically producing hydrogen gas from organic waste by anaerobic fermentation of the organic waste with at least one strain of yeast.

Abstract: Exemplary methods of producing methane in a reservoir may include accessing a consortium of microorganisms in a geologic formation. The methods may include delivering an aqueous solution including waste product to the consortium of microorganisms. The methods may include increasing production of gaseous materials by the consortium of microorganisms The methods may include recovering gaseous products from the reservoir. The gaseous products may by characterized by an enriched methane concentration.

Abstract: The disclosure relates to a system and method for preflash processing used in dry mill ethanol facilities, including routing beer to a baffled flash tank, in which the beer is processed and then separated into a vapor stream and liquid beer. Preheating the beer via preflash processing efficiently recovers energy within the system, thereby reducing the need for additional energy input.

Abstract: The invention relates to a method for production of tyrosol, wherein a transgenic bacterial cell that heterologously expresses phenylpyruvate decarboxylase and that overexpresses phospho-2-dehydro-3-deoxyheptonate and prephenate dehydrogenase, and wherein pheAL and feaB are both inactivated or removed, is grown in a medium comprising a metabolic precursor of phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P), particularly glucose, and optionally, phenylalanine as a supplement; and tyrosol is extracted from said medium. The invention also relates to a method for production of salidroside, wherein the transgenic cell additionally heterologously expresses uridine diphosphate dependent glycosyltransferase (UGT85A1, EC:2.4.1.

Abstract: The present invention relates to a chemical and biological integrated degradation process for PET, for recycling PET, and, more specifically, the present invention provides a PET upcycling technique for producing a high-value product via a chemical pretreatment process of PET, a TPA and EG production process using an enzyme, and a process for converting TPA and EG to PCA and GLA, respectively.

Abstract: Provided is a recombinant microorganism including at least two genes for producing itaconic acid and its derived monomers, and the at least two genes are located on the same expression vector. The at least two genes include one encoding cis-aconitic acid decarboxylase and the other one encoding aconitase, and the genome of the recombinant microorganism includes a gene encoding the molecular chaperone protein GroELS. Also provided is a method for producing itaconic acid by using the microorganism.

Abstract: The present disclosure provides a method for two-phase partitioning production of a medium-chain fatty acid (MCFA) by dry anaerobic digestion. In the present disclosure, due to a slow heat transfer of the dry anaerobic digestion, a same dry anaerobic digestion device is naturally divided into two phases, and the MCFA is synthesized while producing electron acceptors and electron donors in the same dry anaerobic digestion device. Meanwhile, the dry anaerobic digestion device is provided with a high-efficiency decomposing microbial inoculant on an upper part and inoculated with sludge having a carbon chain extension function on a lower part. In this way, a material residence time is regulated, and cycles of hydrolytic acidification and carbon chain extension are shortened, thereby achieving the high-value conversion of agricultural waste while increasing a conversion rate of organic acids in the dry anaerobic digestion.

Abstract: The invention provides a method for preparing pyrrolidone, and the invention provides a method for catalytically preparing pyrrolidone with ?-aminobutyric acid in the presence of carnitine-CoA ligase CaiC. The carnitine-CoA ligase CaiC has an amino acid sequence as shown in SEQ ID NO:1. The ligase has catalytic activity in the cyclization of ?-aminobutyric acid to produce pyrrolidone. The carnitine-CoA ligase provided in the present invention affords a yield of pyrrolidone of 3.26 g/L and a molar yield of 39.53% in 24 h when ?-aminobutyric acid is used as a substrate, thus reducing the production period, improving the production of pyrrolidone, and accelerating the industrialization process of producing pyrrolidone by enzymatic conversion method.

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 invention provides modular cell-free de-novo synthesis of glycans with immobilized bionanocatalysts. The invention provides materials, and in particular, magnetic materials, for producing glycans of defined length and sequences using one or more enzymes that are immobilized within bionanocatalysts (BNCs) which in turn are embedded within scaffolds to control the synthesis in batch or continuous processes manufacturing. In some embodiments, the scaffolds are high magnetism and high porosity composite blends of thermoplastics or thermosets comprising magnetic particles that form powders. In some embodiments, Selective Laser Sintering (SLS) is used to design and produce objects via 3D printing by sintering composite magnetic powders. The modular flow cells may be mixed and matched for a highly customizable and highly efficient cell-free manufacturing process. In some embodiments the elementary and system modules provided by the invention are employed.

Abstract: The present invention provides a Ganoderma lucidum ?-glucan extract, a preparation method and detection method therefor. The preparation method includes: S1: crushing fruiting bodies of Ganoderma lucidum, mixing the crushed fruiting bodies with a solvent, adding trypsin for enzymatic hydrolysis for 0.5-2 h, and separating to obtain a Ganoderma lucidum fruiting body filter residue; S2: mixing the Ganoderma lucidum fruiting body filter residue with an alkali solution, carrying out ultrasonic extraction with heating, adjusting the pH value of the obtained filtrate to be neutral, and concentrating to obtain a crude Ganoderma lucidum polysaccharide; S3: carrying out alcohol precipitation on the crude Ganoderma lucidum polysaccharide, separating the obtained precipitate, and freeze-drying to obtain a crude Ganoderma lucidum ?-glucan extract; and S4: purifying the crude Ganoderma lucidum ?-glucan extract by glucose gel column chromatography to obtain a Ganoderma lucidum ?-glucan extract.

Abstract: The present invention relates to the production of steviol glycoside rebaudiosides D4, WB1 and WB2 and the production of rebaudioside M from Reb D4.

Abstract: To determine the presence of Mycobacterium in an environment, a sample from the environment can be plated onto a growth medium that is selective for Mycobacterium. Prior to plating, the sample may be treated with a compound containing sodium dodecyl sulfate containing glycine hydrochloride. Plating may occur immediately after the addition of the compound or after a standing period. The agar based growth medium can include a high concentration of crystal violet, in excess of 0.5 ?g/ml. Mycobacterium colonies will generally appear white while other colonies will generally appear stained purple or another color.

Abstract: A growth medium for a biological indicator is provided. The growth medium can include a base growth medium as well as an additive. The additive can include a carbon source unit, such as, but not limited to, glucose, and a volatile organic compound unit. Alternatively, the additive can include a carbohydrate source. The present invention is also directed to a self-contained biological indicator (SCBI) that includes a container, spores disposed on a carrier, a growth medium, and an additive. The additive can include a carbon source unit or a molecule containing a part that can form a VOC when reduced or oxidized, such as, but not limited to glucose, and a volatile organic compound unit. Alternatively, the additive can include a carbohydrate source. It has been found that the addition of such additives to the growth medium facilitates the efficient and accurate detection of a failed sterilization process.

Abstract: Provided are a bacterial colony formation method for sensitive and rapid culture of H. pylori and an effect evaluation method for the same. The bacterial colony formation method comprises primary isolation, cryopreservation and recovery, growth of a single bacterial colony, and subculture. The effect evaluation method provides an effect evaluation index for the H. pylori culture method.

Abstract: A method for determining the anti-biofilm activity of an active agent on a bacterial biofilm. The method comprises culturing a bacterial colony in a culture medium in contact with at least one bead under conditions to form at least one biofilm coated bead. The at least one biofilm coated bead is then separated from planktonic bacteria to provide at least one washed biofilm coated bead substantially free of planktonic bacteria. The washed biofilm coated bead is then aseptically transferred to a vessel such as a well of a well plate. A growth medium, a metabolic dye and a known amount of the active agent of interest are then added to the or each vessel containing a washed biofilm coated bead. The growth medium, metabolic dye, active agent of interest and biofilm coated bead are then incubated in the or each vessel.

Abstract: Described herein are systems for measuring enzymatic activities. Also described herein are methods for measuring or screening enzymatic activities utilizing the systems described herein.

Abstract: Disclosed are composition and methods for treating immune disorders. Also disclosed are diagnosis methods and prognosis methods.

Abstract: The present disclosure relates to materials and methods for spatial detection of nucleic acid in a tissue sample or a portion thereof. In particular, provided herein are materials and methods for detecting RNA so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. In some embodiments, the materials and methods provided herein enable detection of gene expression in a single cell.

Abstract: Means and methods for preparing double stranded target DNA molecules for sequencing. In embodiments double stranded backbone DNA molecules comprising 5? and 3° ends are provided that are: ligation compatible with 5? and 3? ends of the target DNA; form a first restriction enzyme recognition site when self-ligated; in a form that enables self-ligation. Methods may comprise providing, if not already present, the target DNA with 5? and 3? ends that are in a form that prevents self-ligation and that are ligation compatible with the backbone DNA 5? and 3? ends. Methods may further comprise ligating the target DNA to the backbone DNA in the presence of a ligase and a first restriction enzyme that cuts the first restriction enzyme recognition site, thereby producing at least one DNA circle comprising a backbone DNA molecule and a target DNA molecule. Linear DNA.

Abstract: The present disclosure in some aspects relates to methods and compositions for confining molecules generated in a biological sample. In particular examples, rolling circle amplification (RCA) products are generated in a fixed biological sample which has been crosslinked prior to RCA, such that the three-dimensional crosslinked matrix generated prior to RCA confines the RCA products, and the RCA products are smaller than they would otherwise be in a fixed biological sample which has not been crosslinked prior to RCA. Confining the RCA products by generating them in a pre-crosslinked matrix in the biological sample may result in compaction of the RCA products and facilitate subsequent in situ analysis. The sample crosslinking can be performed after probe hybridization to nucleic acid molecules in the sample and before RCA.

Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.

Abstract: The present invention relates to a fluorescent reporter capable of labeling nucleic acids including DNA and exhibiting luminescent properties at an excited energy level, and various uses thereof.

Abstract: The present invention relates to self-phosphorylating deoxyribozymes containing or consisting of the nucleotide sequence: 5?-X1X2X3AX4X5-R1-X6X7X8X9X10-bp1-helix1-R2-helix2-bp2-X11TGACX12TGGGAX13-helix3-X14-R3-3? (SEQ ID NO. 1) wherein X1 is G or T; X2 is G or T; X3 is A or C; X4 is G or T; X5 is A or T; X6 is G or T or A; X7 is A or C or G or T; X8 is A or G or T; X9 is T or C or A or G; X10 is A or T or G; X11 is G or A; X12 is T or C or G; X13 is T or G or C; X14 is G or A or C or T; R1 represents a nucleotide sequence containing 3 to 30 nucleotides; R2 represents a nucleotide sequence containing 3 to 30 nucleotides; R3 represents a nucleotide sequence containing 0 to 30 nucleotides; bp1 and bp2 are nucleotides selected from G, A, C, T, which together form a base pair; helix1, helix2, and helix3 each independently denotes a nucleotide sequence preferably containing 4 or more nucleotides, wherein helix1, helix2, and helix3 together form a triple helical structure.

Abstract: Disclosed herein are methods and compositions for normalizing polynucleotide concentration. Normalizing may be accomplished using polynucleotide binding proteins (e.g., catalytically inactive CRISPR protein or catalytically inactive Argonaute proteins). The polynucleotide binding proteins may bind to the adapter sequences of a target polynucleotide. Thus, adding the same amount of a polynucleotide binding proteins to different samples and then extracting the polynucleotide protein is shown herein to extract similar amounts of target polynucleotides from the different samples.

Abstract: The microRNA detection level decreases when a microRNA-containing biological sample is preserved after being collected. Further, a relatively long period of time is required for dissolving a hydrochloride of a neutral amino acid, which is in the form of crystals, in water. Since a hydrochloride of a neutral amino acid is an acidic substance, and causes skin irritation and mucosal irritation, the handling of the hydrochloride requires safety precautions. The present invention provides a method of detecting a microRNA in a biological sample, the method including the steps of: mixing an acid with the biological sample, preserving the resulting mixture for a predetermined period of time, collecting the microRNA in the biological sample, and detecting the microRNA. Further, the present invention provides a homogeneous semi-solid composition composed of a hydrochloride of a neutral amino acid, water and an alcohol.

Abstract: Colorimetry is used to detect amplification reaction products. A sample is contacted with a reaction mix under conditions such that an amplification reaction occurs and produces an amplification reaction product if the sample contains a target nucleic acid template molecule. The reaction mix includes an enzyme for catalyzing the amplification reaction, and at least one halochromic agent. If the target nucleic acid template molecule is present, the amplification reaction changes the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating the presence of the target nucleic acid. If the target nucleic acid template molecule is not present, the amplification reaction does not generate an adequate number of protons to sufficiently change the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has not been produced.

Abstract: The present disclosure provides devices, systems, methods for processing and/or analyzing a biological sample. An analytic device for processing and/or analyzing one or more biological samples may be electronically and/or physically configured or programed to activate one or more features/operations of the analytic device. The analytic device can be configured or programed by one or more instructions received from a cooperating electronic device or a remote server. The analytic device may comprise a moving carriage. The analytic device may be portable. The analytic device may receive instructions for performing an assay from a mobile electronic device external to a housing of the analytic device.

Abstract: In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating sequence variation between different alleles. More specifically, in some embodiments, the present invention provides for compositions, methods and kits for quantitating rare (e.g., mutant) allelic variants, such as SNPs, or nucleotide (NT) insertions or deletions, in samples comprising abundant (e.g., wild type) allelic variants with high specificity and selectivity. In particular, in some embodiments, the invention relates to a highly selective method for mutation detection referred to as competitive allele-specific TaqMan PCR (“cast-PCR”).

Abstract: A method for clustering nucleotide strings of DNA strand replicas in clusters, comprising, for each pair of a first nucleotide string and a second nucleotide string, carrying out: arranging a matrix wherein each matrix element corresponds to a selected nucleotide in the first nucleotide string and to a further selected nucleotide in the second nucleotide string and is configured to store a calculated edit value indicative of an edit distance; progressively filling the matrix by storing calculated edit values; if the edit value calculated for a matrix element belonging to an output diagonal of the matrix is not lower than a cluster threshold, stopping said progressively filling and placing said first and second nucleotide strings in two different clusters, said output diagonal comprising the matrix element corresponding to the last column and the last row of the matrix.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: Disclosed is a set of adhesive adapters containing sample barcodes for specifically tagging different samples. Further disclosed is a method for simultaneously detecting CpG methylation in a high number of samples, which is multi-sample reduced-representation bisulfite sequencing (msRRBS); and an alternative method thereof, which is multi-sample reduced-representation APOBEC sequencing (msRRAS). The adapters are used to specifically tag the plurality of samples, including all DNA fragments of the plurality of samples; then the plurality of samples are pooled to allow a single-tube reaction of the plurality of samples; and then the subsequent conversion, sequencing library construction and sequencing, distribution and decoding of readings of each sample, and downstream analysis are conducted. The library construction technology of the present application has advantages such as high efficiency, low cost, and stable and convenient operations.

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 gene analyzer that analyzes a base sequence of a sample manages an observation environment and mobility correction amount data for correcting a position in a time direction of time-series data of signal intensities of a plurality of bases, and executes the following processes including: a process of scaling the mobility correction amount data associated with the observation environment different from a first observation environment to generate default mobility correction amount data when the gene analyzer receives time-series data of signal intensities of a plurality of bases acquired by electrophoresing the sample in the first observation environment; a process of correcting the position in the time direction of the time-series data of the signal intensities of the plurality of bases using an optimization algorithm; and a process of identifying the base sequence of the sample using the corrected time-series data of the signal intensities of the plurality of bases.

Abstract: A method of genotyping includes applying a sample solution including a plurality of copies of a sample polynucleotide to an array of sensors. The sample polynucleotide includes a region associated with an allele. The method further includes measuring using a plurality of sensors of the array of sensors a characteristic of the region of the plurality of copies of the sample polynucleotide and determining using a computational circuitry and the measured characteristics a statistical value indicative of the allele.

Abstract: Methods and compositions for generating sequencing reads by partition of origin. One can introduce a unique molecular identifier and bead-specific barcodes to target nucleic acid fragments and the combination of bead-specific barcode, UMI and fragment can be used to identify when multiple bead-specific barcodes originated in the same partition, allowing for improved deconvolution of partition-based sequence analysis.

Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.

Abstract: Provided herein are reagents, compositions, and methods for sequencing nucleic acids. Among the reagents disclosed are nucleotides labeled with cleavable linkers. Certain linkers are configured to undergo immolation reactions following cleavage, which can generate scars with enhanced properties for nucleic acid sequencing and synthesis. The present disclosure also provides reagents, compositions, and methods for capping scars generated through linker cleavage, which can alter scar properties, and in some cases can increase the rate and accuracy of nucleotide incorporations during polymerization.

Abstract: An example of a nucleic acid sequencing component includes a support. A glycolipid bi-layer is attached to at least a portion of the support. First and second primers are respectively attached to the glycolipid bi-layer. In one example, the support is a substrate of a flow cell. In another example, the support is a core nanostructure that can be introduced into a flow cell.

Abstract: Provided herein are methods for determining levels of cell lysis in samples, particularly sampled in which amounts of non-self cell-free DNA may be determined.

Abstract: This disclosure provides methods and systems for single-cell, multi-omic analysis of target cells without microfluidic devices. The disclosed methods involve the use of template particles to template the formation of monodisperse droplets to generally capture a single target cell from a population of cells in an encapsulation, derive a plurality of distinct mRNA molecules from the single target cell, and quantify the distinct mRNA molecules to generate an expression profile. Nucleic-acid-tagged antibody conjugates are used for simultaneous proteomic analysis along with the gene expression profiling.

Abstract: A process for analysing chromosome interactions relating to immunotherapy of cancer.

Abstract: The present disclosure provides methods of amplifying and sequencing DNA, comprising: extracting cell-free DNA from a blood, plasma, serum or urine sample of a transplant recipient who has received transplantation of one or more organs including simultaneous or sequential transplantation of multiple organs, wherein the extracted cell-free DNA comprises donor-derived cell-free DNA and recipient-derived cell-free DNA; performing targeted amplification at 200-50,000 target loci in a single reaction volume using 200-50,000 primer pairs, wherein the target loci comprise polymorphic loci and non-polymorphic loci; sequencing the amplification products by high-throughput sequencing to obtain a sequencing reads and quantifying the amount of donor-derived cell-free DNA and the amount of total cell-free DNA based on the sequencing reads; and determining whether the amount of donor-derived cell-free DNA or a function thereof exceeds a cutoff threshold indicating transplant rejection or graft injury.