Abstract: [Problem] To provide a novel expression vector capable of effectively expressing a target protein in mitochondria and suppressing undesirable expression of the target protein in cell organelles other than mitochondria. [Solution] The present invention provides a recombinant expression vector for expressing a target protein in mitochondria of animal cells, and a lipid membrane structure having the vector encapsulated therein, wherein the recombinant expression vector has a promoter sequence exhibiting a transcription activity in the nuclei of animal cells, and has, under the control of the promoter sequence, a coding region which codes a target protein and includes one or more TGAs as codons corresponding to tryptophan. The recombinant expression vector according to the present invention can more efficiently and selectively express a target protein in mitochondria, and can be used as a more safe and effective drug for treating mitochondrial diseases.

Abstract: Compositions and methods are provided for lowering cholesterol in a subject are provided. An adeno-associated viral vector is provided which includes a nucleic acid molecule comprising a sequence encoding anti-PCSK9 antibody. In desired embodiments, the subject is a human.

Abstract: The present invention relates to a new method for successfully inducing the mutation of cell chemokine receptor CCR5 gene into CCR5?32 deletion gene by using the CRISPR-Cas9 genome editing technique. CCR5 is an important co-receptor for entry of Human Immunodeficiency Virus (HIV) into human host cells. CCR5?32 deletion is a 32-bp deletion in CCR5 coding region, which results in change and premature termination in the sequence following the 185th amino acid. Biallelic homozygous deletion of CCR5?32 is naturally resistant to HIV infection, i.e., the people carrying this mutation can't be infected by HIV. The present invention uses both lentiviral packaging system and the CRISPR technique to induce CCR5?32 deletion. Due to the characteristics of a wide range of lentivirus infection, the invention can be applied to cells such as bone marrow stem cells and CD4+ T cells and can be expected to be the therapeutic drug for HIV/AIDS infection or other diseases.

Abstract: The invention provides lentiviral preparations containing a sulfonic acid buffer, such as 1,4-piperazinediethanesulfonic acid (PIPES), 2-(N-morpholino)ethanesulfonic acid (MES), and 3-morpholinopropane-1-sulfonic acid (MOPS), a sodium citrate buffer, or a phosphate buffer. The invention additionally encompasses methods of lentiviral purification as well as methods of transducing human cells.

Abstract: The present invention provides methods and compositions for labeling and/or targeting cells with increased calcium by providing a CREB reporter system. In addition, methods of treating disorders with activated cells such as brain disorders or cancer are also provided herein.

Abstract: The present invention provides methods and compositions for improving the efficacy of viral transduction of cells. More particularly, the present invention provides methods and materials useful for safely and reliably improving the efficiency of methods for transducing cells, such as human hematopoietic stern cells (HSC), with viruses and/or viral vectors. The compositions and methods are useful for therapeutic indications amenable to treatment with hematopoietic stem cell gene therapies.

Abstract: Cancer immunotherapy is enhanced by co-expression of cancer associated or tumor-specific (neo)epitopes with co-stimulatory molecules and/or other immune activators. Where desired, treatment may be enhanced by administration of a immune checkpoint inhibitor.

Abstract: The present invention provides a recombinant turkey herpesvirus modified by the presence of the cDNA encoding the hemagglutinin protein of avian influenza virus under a promoter. A poultry vaccine comprising the recombinant turkey herpesvirus described in the present invention can induce serological responses that may be easily detected by the hemagglutination inhibition assay but not by commercially available diagnostic ELISA kits; thus enabling easy differentiation between vaccination and field infection.

Abstract: The present invention relates to a method for inducing the transdifferentiation of B lymphoid cells into T lymphoid cells using transcription factor Hoxb5, and related products and applications thereof. The method of the present invention specifically comprises: introducing Hoxb5, a nucleic acid molecule encoding Hoxb5 or a construct comprising the nucleic acid molecule into the B lymphoid cells to obtain the B lymphoid cells with overexpressed Hoxb5; then implanting the obtained B lymphoid cells into the body of a subject to obtain regenerated T cell progenitor cells by way of transdifferentiation, and then the T cell progenitor cells differentiate into mature T cells with functions. The regenerated T cells obtained using the method of the present invention are not only functionally normal, but also show no risk of tumorigenesis or extremely low risk of tumorigenesis.

Abstract: The present invention provides methods and compostions to improve the efficiency of somatic cell nuclear transfer (SCNT) and the consequent production of nuclear transfer ESC (ntESC) and transgenic cells and/or non-human animals. More specifically, the present invention relates to the discovery that trimethylation of Histone H3-Lysine 9 (H3K9me3) in reprogramming resistant regions (RRRs) in the nuclear genetic material of donor somatic cells prevents efficient somatic cell nuclear reprogramming or SCNT. The present invention provide methods and compositions to decrease H3K9me3 in methods to improve efficacy of SCNT by exogenous or overexpression of the demethylase Kdm4 family and/or inhibiting methylation of H3K9me3 by inhibiting the histone methyltransferases Suv39h1 and/or Suv39h2.

Abstract: The present disclosure provides modified site-directed modifying polypeptides, and ribonucleoproteins comprising the modified polypeptides. The modified site-directed modifying polypeptides are modified for passive entry into target cells. The modified site-directed modifying polypeptides are useful in a variety of methods for target nucleic acid modification, which methods are also provided.

Abstract: Describes is a fermentation method for producing a hydrocarbon compound comprising the culturing of an organism in a liquid fermentation medium, wherein said organism produces a desired hydrocarbon compound by an enzymatic pathway, said enzymatic pathway comprising an intermediate which evaporates into the gaseous phase and wherein said intermediate is recovered from the gaseous phase and is reintroduced into the liquid fermentation medium.

Abstract: This invention relates to the use of a yeast strain overexpressing at least the following genes: the ALK3 gene, at least one of genes ADH2 and ADH5 and at least one of genes FALDH3 and FALDH4, or gene FA01, for the fermentation-based production of carboxylic diacids.

Abstract: A non-naturally occurring eukaryotic or prokaryotic organism includes one or more gene disruptions occurring in genes encoding enzymes imparting increased fumarate, malate or acrylate production in the organism when the gene disruption reduces an activity of the enzyme. The one or more gene disruptions confers increased production of acrylate onto the organism. Organisms that produce acrylate have an acrylate pathway that at least one exogenous nucleic acid encoding an acrylate pathway enzyme expressed in a sufficient amount to produce acrylate, the acrylate pathway comprising a decarboxylase. Methods of producing fumarate, malate or acrylate include culturing these organisms.

Abstract: High levels of polyhydroxyalkanoates (PHA) can be produced from wastewater comprising Readily Biodegradable COD (RBCOD) using activated sludge comprising microorganisms capable of accumulating PHA by contacting the wastewater with the activated sludge in the presence of dissolved oxygen during a first period of time, to obtain PHA-loaded activated sludge, and then supplying elements essential for growth such as nitrogen and phosphorus and allowing up-take of these elements and limited growth during a second period of time, the supplied amount of at least of one of said essential elements compared to the amount of RBCOD supplied in step a) limiting the growth to an extent that not all PHA is used for growth, to obtain grown activated sludge; and removing or harvesting part of the PHA-loaded activated sludge and/or part of the grown activated sludge, so that the total average retention time of the sludge is less than 72 h.

Abstract: The present invention relates to polynucleotides encoding novel fusion polypeptides essentially composed of a signal peptide for membrane translocation and a polypeptide providing ?-1,6-glucosidase activity and to bacteria containing said polynucleotides. The invention further relates to methods for producing fine chemicals using media containing isomaltose and/or panose as carbon source.

Abstract: Disclosed are methods of making a modified lecithin by conducting an enzymatic conversion of a naturally derived lecithin to form a modified lecithin, e.g., having an enhanced level of phosphatidylethanolamine, phosphatidylserine, or a combination thereof. Compositions prepared from the modified lecithin and use to inhibit lipid oxidation are described.

Abstract: Methods of generating oligosaccharides are provided.

Abstract: A process for producing alcohol from lignocellulosic biomass includes adding at least one of sulfur dioxide and sulfurous acid to the lignocellulosic biomass to provide an effective sulfur dioxide dosage and/or effective sulfur dioxide slurry concentration, each of which is calculated using the ratio of the volume of the slurry in the pretreatment reactor to the total volume of the pretreatment reactor, within a predetermined range.

Abstract: The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a heterocyclic compound. The present invention also relates to methods of using the compositions.

Abstract: The invention relates to improved RNA compositions for use in therapeutic applications. The RNA compositions are particularly suited for use in human therapeutic application (e.g., in RNA therapeutics). The RNA compositions are made by inproved processes, in particular, improved in vitro-transcription (IVT) processes. The invention also relates to methods for producing and purifying RNA (e.g, therapeutic RNAs), as well as methods for using the RNA compositions and therapeutic applications thereof.

Abstract: The present invention provides a method of detecting a Mycobacterium-specific metabolite in the form of mycothiol in a biological sample in vitro, including the steps of preparing a reaction mixture by combining the biological sample with an enzymatic solution containing a reaction buffer, nicotinamide adenine dinucleotide (NAD) and a formaldehyde dependent mycothiol dehydrogenase (FD-MDH); allowing reduction of NAD in the reaction mixture by interaction of FD-MDH with a predetermined Mycobacterium-specific metabolite in the form of mycothiol if present in the biological sample; and detecting reduced NAD within the sample, indicative of the presence of mycothiol in the biological sample and thus of a Mycobacterium infection in the source of the biological sample.

Abstract: A method is described for the identification of multi-subunit biocomplex drug targets. The method includes identifying a target that performs a biological function, wherein the target comprises one or more subunits, wherein a minimum number of the one or more subunits is inactivated to inhibit the biological function. The method includes selecting a drug that binds specifically to each subunit of the one or more subunits with a target probability. The method describes a relationship between inhibition efficiency of the drug and total number of the one or more subunits using a binomial distribution, wherein the inhibition efficiency comprises a probability that the delivered drug blocks the biological function. The method includes confirming empirically the relationship using an experimental target. The method includes administering the drug to the target to treat a multi-drug resistant disease, wherein the target comprises a biological complex in a mammalian subject.

Abstract: The present application is directed to biosensors and methods for detecting a microorganism target in a sample using a mechanically interlocked nucleic acid catanane, wherein an enzyme from the microorganism target or that is activated by a molecule from the microorganism target cleaves a linkage in a first single-stranded nucleic acid ring of the catanane structure, allowing rolling-circle amplification to occur and the presence of rolling-circle amplification products indicates the presence of the microorganism in the sample.

Abstract: The present invention relates to pathogen cleaning and simulation of pathogen spreading. More particularly, some implementations of the described invention relate to systems and methods for spraying materials in a manner that mimics the spreading of pathogens from coughing or sneezing. Some implementations further relate to using a non-aerosol sprayer that produces both a mist and droplets of a mixture containing water, a fluorescent marker, a surfactant, and an antifoaming agent. In some cases, the pump sprayer defines an internal compartment that includes the mixture. In some cases, the sprayer further includes a pump mechanism that is configured to be pumped to compress a gas within the compartment and a release valve that is configured to release pressure within the compartment through a spray nozzle of the sprayer such that droplets and mist of the mixture are sprayed from the nozzle. Other implementations are also described.

Abstract: Methods for determining whether certain compounds, in particular crystals, are present in a sample of a biological fluid that indicates an individual has a particular disease or condition, such as but not limited to gout, pseudogout or urinary tract stones. In some embodiments, the methods include the steps of digestion and filtration of a sample of synovial fluid in order to isolate, if present, monosodium urate monohydrate (MSU), calcium pyrophosphate dihydrate (CPPD), or calcium phosphate crystals from the sample, wherein the filtrate is analyzed with a Raman device to ascertain the presence and type of the crystals. Devices for performing steps of the method are disclosed.

Abstract: Bacteria, systems and methods comprising two-component sensor systems used to detect thiosulfate are described. The systems can be applied to monitoring gut bacteria.

Abstract: The present invention relates to stabilization of one or more component of a PCR or RT-PCR reaction mixture at ambient temperatures. In particular, formulations, compositions, articles of manufacture, kits and methods for substantially stable storage of one or more component of a PCR or RT-PCR reaction mixture at ambient temperatures are provided.

Abstract: The present invention provides a composition and method for stabilizing ribonucleic acid (RNA) from biological samples such that the ribonucleic acid within the sample remains stable at room temperature. The composition comprises an anionic detergent and a buffering agent at a pH of about 5 to about 8.2 and is used in methods for extracting and storing ribonucleic acid from the biological sample.

Abstract: Provided is a method for producing a cell contained base, the method being capable of providing a cell contained base highly accurately controlled in number of nucleic acid molecules contained in a low-concentration nucleic acid standard sample, the method including a liquid droplet discharging step of discharging a cell suspension in the form of a liquid droplet with a liquid droplet discharging unit onto a base including at least one cell contained region; a cell number counting step of counting a number of cells contained in the liquid droplet with a plurality of sensors from two or more directions while the liquid droplet is flying into the cell contained region; and a liquid droplet landing step of landing the liquid droplet in the at least one cell contained region in a manner that a predetermined number of cells are located in the at least one cell contained region.

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: The invention relates to a method of determining an infection of a patient with Enterobacter species potentially resistant to antimicrobial drug treatment, a method of selecting a treatment of a patient suffering from an antibiotic resistant Enterobacter infection, and a method of determining an antibiotic resistance profile for bacterial microorganisms of Enterobacter species, as well as computer program products used in these methods. In an exemplary method, a sample (1), is used for molecular testing (2), and then a molecular fingerprint (3) is taken. The result is then compared to a reference library (4), and the result (5) is reported.

Abstract: Monitoring, analysis and control of fermentation activities includes methods and corresponding systems directed toward agriculture, biofuels, and food production. Complex methods and corresponding systems are provided for classifying a microorganism; profiling a microbiome; sequencing multiple libraries in a single sequencing run; determining a microbiome profile in a sample; and analyzing a material from a location associated with a fermentation process. Additional implementations are directed to methods and corresponding systems for obtaining, deriving, predicting and evaluating microbiome information; control, analysis and direction of fermentation operations; and evaluating, analyzing and displaying microbiome related information in two and three dimensional plots. Yet additional methods and corresponding systems permit identification and analysis of microorganisms capable of imparting beneficial properties to phases of fermentation processes.

Abstract: Methods of detecting the presence of microorganisms in a sample, the methods including combining a sample, a reducing agent, an oxidant generator and a chemiluminescent agent, and in some cases a shielding agent, wherein the reducing agent both reduces the oxidant generator to produce an oxidant and reduces one or more disulfide bonds on a surface of a microorganism and wherein the oxidant oxidizes the chemiluminescent agent to produce a luminescent compound; and detecting the presence or absence of a signal to indicate the presence or absence of microorganisms in the sample, wherein the intensity of the chemiluminescent signal is inversely proportional to the amount of microorganisms in the sample.

Abstract: Provided herein are biomarkers that can be altered in the gut of a mammal having CDI. One or more biomarkers can be used to predict Clostridium difficile infection (CDI) treatment outcome (e.g., response to primary CDI treatment and/or risk of recurrence after primary CDI treatment) in a mammal (e.g., a human) having CDI. Methods for using one or more biomarkers can be used to predict response to primary CDI treatment in a mammal having CDI. Methods for using one or more biomarkers can be used to predict risk of recurrence in a mammal having CDI. Also provided are methods of treating CDI.

Abstract: The present invention provides kits and primers for colony multiplex PCR for the detection of class A, B, C, and D ?-lactamase genes. The rapid detection of bla genes by using the kits and primers according to the present invention allows appropriate prescribing of antibiotics, which can reduce patient mortality and minimize antibiotic resistance. The present invention provides kits and primers for a rapid and accurate molecular method to overcome (a) to detect all clinically-important bla genes and (b) to explain phenotypic tests' results well by using 54 primer pairs, which are designed through novel and elaborate optimization processes. With perfect specificity and sensitivity in 172 control strains and 403 clinical strains, the present invention provides prompt and clinical application to the identification of all bla genes in bacterial pathogens.

Abstract: Provided are methods and compositions for detecting a target analyte suspected to be present in a sample with background molecules using a nanopore device. A plurality of probes for polymer scaffold identification or for target analyte binding and detection are provided.

Abstract: Disclosed are compositions and a method relating to amplifying and detecting nucleic acids.

Abstract: This disclosure relates to methods, compositions, and related apparatuses for detection and quantification of nucleic acid molecules associated with a solid surface. Methods can include detecting or quantifying at least one nucleic acid molecule associated with a surface by contacting the at least one nucleic acid molecule with a fluorophore, wherein the fluorophore emits increased fluorescence at a wavelength when in contact with nucleic acid molecule, and detecting or measuring fluorescence from the fluorophore at the wavelength. Compositions can comprise a fluorophore and a nucleic acid molecule, wherein the nucleic acid molecule is associated with a surface, and the fluorophore has the property of emitting increased fluorescence at a wavelength when in contact with a nucleic acid molecule.

Abstract: Described herein are methods and systems for detecting DNA or RNA using single molecules array or other techniques. DNA or RNA from the sample may be fragmented and exposed to a first type of binding ligand and a second type of binding ligand that comprise nucleic acid sequences complimentary at least a portion of a sequence contained in the target DNA or RNA. At least a portion of the fragmented DNA or RNA associates with at least one of the first type of binding ligand and/or the second type of binding ligand, wherein the first type of binding ligand and second type of binding ligand comprises nucleic acid sequences complimentary to a different portions of a sequence contained in the DNA or RNA. A portion of the sample exposed to the binding ligands is analyzed to determine the number of fragmented DNA or RNA sequences.

Abstract: In some aspects, the present disclosure provides methods for forming ligation products comprising single-stranded polynucleotides. Ligation products formed by various aspects of the present disclosure can be useful for various applications, including but not limited to sequence analysis. In some embodiments, the ligation products comprise cell-free polynucleotides. In some aspects, the present disclosure provides reaction mixtures, kits and complexes consistent with the methods herein.

Abstract: The invention relates to a method for confirming an amplified nucleic acid target sequence (target sequence), preferably from human samples, during a multiplication reaction in a collective and continuous reaction batch as a one-pot process, wherein the confirmation of the target sequence amplification product is obtained by means of a hapten-pair-marked artificial template amplification product. The artificial template sequence is amplified and optionally marked by means of the 5?-cleavage products of the at least one target-sequence-specific FEN probe. The 5?-cleavage product of the at least one target-sequence-specific FEN probe is obtained only if the FEN probe hybridizes, by means of the target-sequence-specific 3? sequence thereof, to a complementary sequence segment of the at least one target sequence. The detection of the obtained plurality of template amplification products occurs distinctly and preferably by means of immunochromatographic methods.

Abstract: Methods and compositions for detecting genetic instability using digital amplification assays. The methods may be performed in a set of isolated volumes and generally may involve competitive hybridization of a competitor and a probe/primer with a normal allele and one or more mutant alleles of a microsatellite locus. The competitor may be configured to compete similarly with, or to outcompete, the primer/probe for hybridization with the normal allele. The primer/probe may be configured to outcompete the competitor for hybridization with various mutant alleles of the locus that alter the length of the repetitive sequence by different amounts. Isolated volumes in which the primer/probe outcompetes the competitor may be enumerated, and represent one or more of the mutant alleles. The methods may enable diagnosing microsatellite instability and treating a subject based on the diagnosis.

Abstract: The invention provides an exonuclease or an enzymatically active fragment thereof, said exonuclease having the amino acid sequence of SEQ ID NO:1 or an amino acid sequence which is at least about 50% identical thereto, wherein said exonuclease or enzymatically active fragment thereof (i) is substantially irreversibly inactivated by heating at a temperature of about 55° C. for 10 minutes in a buffer consisting of 10 mM Tris-HCl, pH 8.5 at 25° C., 50 mM KCl and 5 mM MgCl2; (ii) is substantially specific for single stranded DNA; and (iii) has a 3?-5? exonuclease activity. The invention further provides a method of removing single stranded DNA from a sample, a method of nucleic acid amplification, a method of reverse transcription and a method of nucleic acid sequence analysis in which the exonuclease or enzymatically active fragment thereof is used.

Abstract: According to one embodiment, a method of quantifying a target nucleic acid containing a first sequence in a sample is provided. The method includes preparing a substrate on which a plurality of detection regions are arranged, forming a reaction field by placing, on the substrate, a reaction liquid containing a sample, a primer set, and an amplification enzyme, maintaining the reaction field in an isothermal amplification condition, detecting a detection signal for each of the detection regions, determining, for each of the plurality of detection regions, whether positive or negative and detecting or quantifying the target nucleic acid based on the number of positive and/or a rise time of each of the positive detection signal.

Abstract: The present invention provides for stable nucleotide reagents used for nucleic acid amplification by PCR and RT-PCR (Reverse Transcriptase-PCR) that comprises nucleoside polyphosphates having four or more phosphates. The present invention also provides for methods for using the nucleoside polyphosphates having four or more phosphates for detecting the presence or absence of a target nucleic acid sequence in a sample in an amplification reaction.

Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.

Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a NEAR reaction.

Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.

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