Abstract: The invention relates to protease enzymes (that can be thermostable in some embodiments) with unique cleavage specificity as well as their production, isolation, activation and applications. These enzymes can be engineered for quick production and purification. The peptides produced by the action of these protease enzymes have unique properties for biochemical determination of protein sequence. In particular, using the steps of protease digestion, ionization of the specifically produced peptides and fragmentation of these peptides in a mass spectrometer, the amino acid sequence of the peptide may be read as a ladder from the N-terminus.

Abstract: This invention relates to polypeptides having aldolase activity, including pyruvate activity such as, without limitation, HMG and/or KHG aldolase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In some embodiments, the invention is directed to polypeptides having aldolase activity, including pyruvate activity such as, without limitation, HMG and/or KHG aldolase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides in accordance with the invention can be used in a variety of pharmaceutical, agricultural and industrial contexts.

Abstract: Synthetic polynucleotides encoding human methylmalonyl-CoA mutase (synMUT) and exhibiting augmented expression in cell culture and/or in a subject are described herein. An adeno-associated viral (AAV) gene therapy vector encoding synMUT under the control of a liver-specific promoter (AAV2/8-HCR-hAAT-synMUT-RBG) successfully rescued the neonatal lethal phenotype displayed by methylmalonyl-CoA mutase-deficient mice, lowered circulating methylmalonic acid levels in the treated animals, and resulted in prolonged hepatic expression of the product of synMUT transgene in vivo, human methylmalonyl-CoA mutase (MUT).

Abstract: Fusion proteins having thermostable blunt-end ligase activity are provided. Blunt-end ligases are useful for DNA amplification, sequencing, production of recombinant DNA and recombinant fusion proteins, and other purposes. These thermostable blunt-end DNA ligases are useful in ligation schemes which include, e.g., an incubation at about 60-65° C. or higher, or as high as about 94° C., or at other temperatures. The ligases disclosed herein may enable high temperature blunt-end ligation without need for molecular crowding agents, and so may be useful for many nucleic acid ligation-amplification schemes, e.g., ones which operate at a uniform temperature (e.g., at about 60° C. or higher), including ones which require temperature cycling, e.g., from about 94° C. to about 60° C. (or higher) for one, two, three, or more cycles.

Abstract: A solid substrate for biological sample storage under dry-state and elution of biomolecules is provided. The dry, solid substrate comprises a surface modified with a plurality of hydrophilic groups; and the substrate is comprised of one or more protein denaturing agents impregnated therein under a substantially dry state. A method for elution of biomolecules from biological samples is also provided. The compositions disclosed herein provide for enhanced elution and recovery of biomolecules, such as nucleic acids, from the sample. The sample is disposed on a substrate, dried to a substantially dry state; eluted from the biological sample dried on the substrate by rehydrating the substrate in an elution buffer.

Abstract: The present invention relates the use of broad range primer (e.g., as broad range capture olignucleotides) immobilized in a SCODA method gel to allow, for example, selective concentration of target nucleic acids. Such concentrated target nucleic acids may, for example, be: i) eluted from the gel and analyzed (e.g., by broad range primer methods); ii) subject to in situ (e.g., in gel) PCR methods; and/or iii) analyzed in the gel (e.g., by fluorescent detection methods).

Abstract: A method is provided for generating RNA nanoparticles having modified nucleotides and/or having increased nuclease resistance where the RNA nanoparticles are formed cotranscriptionally by T7 RNA polymerase in the presence of manganese ions.

Abstract: Disclosed are RNA constructs which function to activate or inactivate a biological process, e.g., may be designed for attachment to a polypeptide coding region. Such RNA constructs modulate translation of a polypeptide from the coding region in response to the presence of a target polynucleotide in an expression environment. Such RNA constructs include a weakened stem-loop structure which, when bound to the target polynucleotide, assumes stem-loop secondary structure and associates with an RNA binding protein. Association with the RNA binding protein modulates translation of the polypeptide coding region. Such RNA constructs also have three-way junction joining regions 3? and 5? of the stem-loop structure.

Abstract: The present invention relates to the identification of a microRNA family, designated miR-29a-c, that is a key regulator of fibrosis in cardiac tissue. The inventors show that members of the miR-29 family are down-regulated in the heart tissue in response to stress, and are up-regulated in heart tissue of mice that are resistant to both stress and fibrosis. Also provided are methods of modulating expression and activity of the miR-29 family of miRNAs as a treatment for fibrotic disease, including cardiac hypertrophy, skeletal muscle fibrosis other fibrosis related diseases and collagen loss-related disease.

Abstract: The present invention relates to the identification of a microRNA family, designated miR-29a-c, that is a key regulator of fibrosis in cardiac tissue. The inventors show that members of the miR-29 family are down-regulated in the heart tissue in response to stress, and are up-regulated in heart tissue of mice that are resistant to both stress and fibrosis. Also provided are methods of modulating expression and activity of the miR-29 family of miRNAs as a treatment for fibrotic disease, including cardiac hypertrophy, skeletal muscle fibrosis other fibrosis related diseases and collagen loss-related disease.

Abstract: The present invention relates to the identification of a microRNA family, designated miR-29a-c, that is a key regulator of fibrosis in cardiac tissue. The inventors show that members of the miR-29 family are down-regulated in the heart tissue in response to stress, and are up-regulated in heart tissue of mice that are resistant to both stress and fibrosis. Also provided are methods of modulating expression and activity of the miR-29 family of miRNAs as a treatment for fibrotic disease, including cardiac hypertrophy, skeletal muscle fibrosis other fibrosis related diseases and collagen loss-related disease.

Abstract: Materials and methods for regulating gene expression using nanoparticles functionalized with antisense oligonucleotides are provided.

Abstract: Methods and compositions are provided for the treatment of a mitochondrial disease in an individual with the mitochondrial disease. Aspects of the methods include administering an inhibitor of a Pumilio-like protein and/or an inhibitor of a serine/arginine-rich family of pre-mRNA splicing factor (SR) protein to a subject. Also provided are methods, compositions, systems and kits for transdifferentiating target cells to neurons, which find use in producing neurons for the development of new therapies, for experimental evaluation, as a source of lineage- and cell-specific products, and the like, for example, for use in treating human disorders of the CNS.

Abstract: Novel oligonucleotide pairs which can form a duplex comprising one or more DNA-like nucleotides (e.g., 2?-substituted arabinonucleotides (ANA)); in combination with one or more RNA-like nucleotides (e.g., 2?-substituted ribonucleotides (RNA) and/or locked nucleic acid nucleotides (LNA)), are disclosed. The use of such oligonucleotide duplexes, such as for silencing the expression of a nucleic acid or gene of interest using small interfering RNA (siRNA) technologies, is also disclosed.

Abstract: Efficient sequence specific gene silencing is possible through the use of RNAi technology. By selecting particular RNAi molecules by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of RNAi molecules are disclosed including those directed to nucleotide sequences for CNTD2.

Abstract: The present invention relates to a composition for preventing or treating diseases associated with human papillomavirus (HPV), and more specifically, cancer associated with HPV, and even more specifically, cervical cancer. The nucleotide sequence of the present invention, the sequence in which the base thereof is modified, and a specific combination thereof can be useful in a composition for effectively treating diseases associated with HPV infection by greatly inhibiting the expression of the E6/E7 gene of HPV type 16 or 18.

Abstract: Efficient sequence specific gene silencing is possible through the use of RNAi technology. By selecting particular RNAi molecules by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of RNAi molecules are disclosed including those directed to nucleotide sequences for SEC61G.

Abstract: Disclosed herein are an expression vector capable of expressing myrcene, an Escherichia coli strain transformed with the vector and having improved capability of producing myrcene and a method for producing myrcene and a method for recycling glycerol using the same. In an aspect, the transformed Escherichia coli strain of the present disclosure can produce myrcene with high purity on a large scale using glycerol or glucose as a carbon source. Also, the Escherichia coli strain of the present disclosure is economical and environment-friendly because it can produce high value-added myrcene using waste glycerol as a carbon source. In addition, the strongly volatile myrcene can be produced and isolated at the same time.

Abstract: The invention provides a system of heavy metal sequestration by bacteria. The bacteria expresses the ppk, mt, and/or ?-galactosidase (lacZ) genes and can tolerate at least 25 ?M mercury, 1,000 ?M zinc, 250 ?M cadmium, and 3,000 ?M Pb. The system allows for facile determination of the presence of heavy metal contaminants in a liquid and the facile collection of the bacteria that has sequestered large amounts of heavy metal. Further provided is a system of gene expression in bacteria that comprises phage and plastid gene expression elements and delivers a particularly high level of protein expression and heavy metal resistance.

Abstract: The present disclosure discloses a vector that can be used for both cyanobacteria and E. coli, which contains, sequentially, a pUC replication origin as a replication origin; a spectinomycin-resistant gene as a selection marker; and a promoter selected from a group consisting of a trc promoter, a tetA promoter or a modified tetA promoter, a BAD promoter and a cbbL promoter. An industrially useful substance may be produced effectively using a host cell transformed with the vector. Also, the vector may be used to insert a variety of target genes through simple combination and, as a result, various vectors can be prepared effectively.

Abstract: The present invention provides for novel metabolic pathways to reduce or eliminate glycerol production and increase product formation. More specifically, the invention provides for a recombinant microorganism comprising a deletion of one or more native enzymes that function to produce glycerol and/or regulate glycerol synthesis and one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to convert a carbohydrate source, such as lignocellulose, to a product, such as ethanol, wherein the one or more native and/or heterologous enzymes is activated, upregulated, or downregulated.

Abstract: The invention relates to gene expression regulatory sequences from soybean, specifically to the promoter of a soybean copper chaperone homolog gene and fragments thereof and their use in promoting the expression of one or more heterologous nucleic acid fragments in a constitutive manner in plants. The invention further discloses compositions, polynucleotide constructs, transformed host cells, transgenic plants and seeds containing the recombinant construct with the promoter, and methods for preparing and using the same.

Abstract: The invention relates to gene expression regulatory sequences from soybean, specifically to the promoter of a soybean actin depolymerizing factor gene and fragments thereof and their use in promoting the expression of one or more heterologous nucleic acid fragments in a constitutive manner in plants. The invention further discloses compositions, polynucleotide constructs, transformed host cells, transgenic plants and seeds containing the recombinant construct with the promoter, and methods for preparing and using the same.

Abstract: The invention relates to gene expression regulatory sequences from soybean, specifically to the promoter of a soybean eukaryotic glyceraldehyde-3-phosphate dehydrogenasegene and fragments thereof and their use in promoting the expression of one or more heterologous nucleic acid fragments in a constitutive manner in plants. The invention further discloses compositions, polynucleotide constructs, transformed host cells, transgenic plants and seeds containing the recombinant construct with the promoter, and methods for preparing and using the same.

Abstract: Methods and compositions are provided which allow for a single microRNA (miRNA) to reduce the level of expression of at least two members of the same protein and/or gene family. While a single 21 base pair miRNA can cause cleavage of a variety of species of mRNAs, an entire gene family cannot be silenced unless that gene family shares near identity within a 21 base pair region that is also able to be cleaved by a single miRNA. In certain embodiments, all members of a given protein and/or gene family can be suppressed with a miRNA expression construct disclosed herein even if they do not share near identity within a 21 base pair region that is also able to function as a miRNA. Such methods and compositions employ miRNA expression constructs having a structure such that the most abundant form of miRNA produced from the construct is a 22-nucleotide miRNA.

Abstract: Four genes, A622, NBB1, PMT, and QPT, can be influenced for increasing nicotinic alkaloid levels in Nicotiana plants, as well as for synthesizing nicotinic alkaloids in non-nicotine producing plants and cells. In particular, overexpressing one or more of A622, NBB1, PMT, and QPT may be used to increase nicotine and nicotinic alkaloid levels in tobacco plants. Non-nicotine producing cells can be engineered to produce nicotine and related compounds by overexpressing A622 and NBB1.

Abstract: The present invention is directed to plants that display an improved oil quantity phenotype or an improved meal quality phenotype due to altered expression of an IMQ nucleic acid. The invention is further directed to methods of generating plants with an improved oil quantity phenotype or improved meal quality phenotype.

Abstract: Certain embodiments are directed to viral production processes for the large scale production of vaccinia virus.

Abstract: Described herein are synonymously altered gene sequences which express protein in differing levels within secretory as compared to non-secretory target tissue. An expression cassette comprising an open reading frame (ORF) for a protein under the control of regulatory sequences which direct expression of the product in cell, which ORF has been modified to preferentially increase expression levels in a selected tissue, wherein the modified ORF is characterized by a triplet frequency of any one of Tables 3-12, 16 or 17.

Abstract: The embodiments disclosed herein relate to the construction of fully-deleted Adenovirus-based gene delivery vectors packaged without helper Adenovirus, and more particularly to their use in gene therapy for gene and protein expression, vaccine development, and immunosuppressive therapy for allogeneic transplantation. In an embodiment, a method for propagating an adenoviral vector includes (a) providing an Adenovirus packaging cell line; (b) transfecting a fully-deleted Adenoviral vector construct into the cell line; and optionally (c) transfecting a packaging construct into the cell line, wherein the fully-deleted Adenoviral vector construct and optionally the packaging construct can transfect the Adenovirus packaging cell line resulting in the encapsidation of a fully-deleted Adenoviral vector independent of helper Adenovirus. In an embodiment, a target cell is transduced with the encapsidated fully-deleted Adenoviral vector for treating a condition, disease or a disorder.

Abstract: Provided are methods for introducing a sequence-specific nuclease into a plant cell comprising a cell wall. Methods are provided for genetically or otherwise modifying plants and for treating or preventing disease in plant cells comprising a cell wall.

Abstract: The invention relates to the use of a protein with recombinase activity to catalyze a site-specific DNA recombination and a method for producing a site-specific DNA recombination. The invention is applicable alone or in combination with other recombinase systems for genetic manipulation, for example in medical research. The objective of the invention is solved by the use of a protein with recombinase activity to catalyze a site-specific DNA recombination at, preferably at two, recognition sites that are identical or reverse complementary to each other. The invention also includes a method for producing a site-specific DNA recombination comprising the steps of a) providing a cell comprising at least two recognition sites that are identical or reverse complementary to each other; and b) contacting a protein with recombinase activity with the recognition sites, thereby producing the site-specific DNA-recombination.

Abstract: The present invention provides a method of increasing production of amorpha-4,11-diene and a method of increasing production of natural rubber. The present invention relates to a method of increasing production of amorpha-4,11-diene which includes the step of attaching an enzyme inhibitor to Arabidopsis thaliana into which has been introduced a gene encoding amorphadiene synthase. The enzyme inhibitor inhibits at least one enzyme other than amorphadiene synthase, that catalyzes an enzymatic reaction in which farnesyl diphosphate acts as a substrate. The present invention also relates to a method of increasing production of natural rubber which includes the step of attaching an enzyme inhibitor to a rubber-producing plant. The enzyme inhibitor inhibits at least one enzyme other than enzymes involved in natural rubber synthesis, that catalyzes an enzymatic reaction in which farnesyl diphosphate acts as a substrate.

Abstract: A multi-stage anaerobic digester is designed to treat a high solids, stackable feedstock. The system may also receive a pumpable feedstock such as a slurry or sludge. In a first stage, the digestate circulates in one direction around a raceway such that the digestate may pass a feed inlet multiple times before leaving the first tank. An optional side stream loop withdraws fibrous material from near the top of the reaceway and return digestate with chopped fibers, preferably lower and further along the raceway. An outlet from the raceway located near, but upstream of the feed inlet discharges partially digested substrate to a second stage, which is operated as a stirred tank reactor. The two stages may be provided in a single tank with an internal wall separating a ring shaped outer portion from a cylindrical inner portion. The digester may be operated in a thermophilic temperature range.

Abstract: The present invention relates to beta-glucosidase that is mutated to have enhanced activity, and a method for producing bioethanol using the same. More particularly, the present invention relates to a polynucleotide encoding beta-glucosidase that is mutated to have enhanced activity, beta-glucosidase expressed from the polynucleotide, an expression vector including the polynucleotide, a transformant that is transformed with the expression vector, a method for producing the mutated beta-glucosidase using the transformant, and a method for producing bioethanol using the transformant. The mutant beta-glucosidase of the present invention increases production of glucose much more than the conventional beta-glucosidase, and thus it can be widely used for economic production of bioethanol.

Abstract: The invention provides a recombinant microorganism that has been genetically engineered to contain metabolic pathway for the production of muconic acid from a salicylic acid intermediate. The genetically engineered metabolic pathway comprises both biosynthetic and biodegradative elements.

Abstract: Recombinant DNA techniques are used to produce oleaginous recombinant cells that produce triglyceride oils having desired fatty acid profiles and regiospecific or stereospecific profiles. Genes manipulated include those encoding stearoyl-ACP desturase, delta 12 fatty acid desaturase, acyl-ACP thioesterase, ketoacyl-ACP synthase, and lysophosphatidic acid acyltransferase. The oil produced can have enhanced oxidative or thermal stability, can be useful as a frying oil, shortening, roll-in shortening, tempering fat, cocoa butter replacement, as a lubricant, or as a feedstock for various chemical processes. The fatty acid profile can be enriched in midchain profiles or the oil can be enriched in triglycerides of the saturated-unsaturated-saturated type.

Abstract: The present invention provides a production method of oxo fatty acid, as well as rare fatty acids such as conjugated fatty acid, hydroxylated fatty acid, partially saturated fatty acid and the like, which uses 4 kinds of enzymes (fatty acid-hydratase, hydroxylated fatty acid-dehydrogenase, oxo fatty acid-isomerase, oxo fatty acid-enone reductase) derived from Lactobacillus plantarum including lactic acid bacteria and the like. Furthermore, the present invention also provides a more efficient production method of oxo fatty acid and the like, which partly uses a chemical oxidation reaction in combination.

Abstract: Disclosed are compositions and methods related to eukaryotic microorganisms that can produce unsaturated fatty acids which can be purified and used.

Abstract: The invention provides a whole cell catalyst which expresses a recombinant ?-dioxygenase or the combination of a recombinant fatty acid reductase and a phosphopantetheinyl transferase phosphopantetheinylating the fatty acid reductase, and which in addition to the ?-dioxygenase and/or the combination of fatty acid reductase and phosphopantetheinyl transferase expresses a transaminase, characterized in that the phosphopantetheinyl transferase and/or transaminase is preferably recombinant; and a method for the conversion of a fatty acid, ?-hydroxy fatty acid, ?-oxo fatty acid or a monoester thereof to an amine, comprising oxidation of the fatty acid, ?-hydroxy fatty acid, ?-oxo fatty acid or the monoester thereof to an oxidation product by contacting with an alkane hydroxylase and/or alcohol dehydrogenase, contacting the oxidation product with a phosphopantetheinylated fatty acid reductase or a ?-dioxygenase to give an aldehyde, and contacting the aldehyde with a transaminase.

Abstract: The invention provides non-naturally occurring microbial organisms containing caprolactone pathways having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce caprolactone. The invention additionally provides methods of using such microbial organisms to produce caprolactone by culturing a non-naturally occurring microbial organism containing caprolactone pathways as described herein under conditions and for a sufficient period of time to produce caprolactone.

Abstract: The present invention relates to mutated and/or transformed microorganisms for the synthesis of various compounds. More specifically, the present invention discloses microorganisms mutated in the genes encoding for the regulators ArcA and IclR. The latter mutations result in a significant upregulation of the genes that are part of the colanic acid operon. Hence, said microorganisms are useful for the synthesis of any compound being part of the colanic acid pathway such as GDP-fucose, GDP-mannose and colanic acid, and/or, can be further used—starting form GDP-fucose as a precursor—to synthesize fucosylated oligosaccharides or—starting from GDP-mannose as a precursor—to synthesize mannosylated oligosaccharides. In addition, mutations in the genes coding for the transcriptional regulators ArcA and IclR lead to an acid resistance phenotype in the exponential growth phase allowing the synthesis of pH sensitive molecules or organic acids.

Abstract: The present invention relates to polypeptides comprising a carbohydrate-binding module amino acid sequence and an alpha-amylase amino acid sequence as well as to the application of such polypeptides.

Abstract: Reaction solutions are disclosed herein comprising water, incompletely refined sucrose, and a glucosyltransferase enzyme that synthesizes insoluble poly alpha-1,3-glucan having at least 50% alpha-1,3 glycosidic linkages and a weight average degree of polymerization (DPw) of at least 100. The yield of poly alpha-1,3-glucan by a reaction solution herein is at least 7% of the weight of sucrose that was converted in the reaction solution. Further disclosed are methods of producing poly alpha-1,3-glucan using incompletely refined sucrose, and poly alpha-1,3-glucan produced by these methods.

Abstract: A plurality of isolated polynucleotide sequences encoding enzymes of the astaxanthin pathway is disclosed. The polynucleotides include: (i) a polynucleotide which encodes Phytoene dehydrogenase (crtI) and a first transcriptional regulatory sequence; (ii) a polynucleotide which encodes Beta-lycopene cyclase (lcy-B) and a second transcriptional regulatory sequence; (iii) a polynucleotide which encodes Beta-carotene ketolase (crtW) and a third transcriptional regulatory sequence; and wherein the first, second and third regulatory sequence are selected such that the expression of the Icy-B and the crtW is greater than a level of expression of the crtI. Methods of generating astaxanthin using the plurality of polynucleotide are also disclosed as well as bacterial cells comprising high levels of astaxanthin.

Abstract: Disclosed is a urine sample analyzer for analyzing particles contained in a urine sample and outputting analytical results. The analyzer includes a flow cell that accepts a measurement specimen, the measurement specimen comprising a urine sample mixed with a reagent, a light irradiation unit positioned to irradiate the flowing measurement specimen with light, a light detector that detects light from individual particles in the flowing measurement specimen, and a data processor that receives signal from the light detector, processes the signal to obtain parameter information corresponding to a length of a cell cluster, and classifies fungi in the measurement specimen into groups by using the parameter information.

Abstract: A method of detecting Listeria monocytogenes. The method comprises providing a culture device with a selective culture medium and a detection article comprising a first indicator system. The selective culture medium facilitates the growth of Listeria microorganisms. When a Listeria microorganism is detected in a sample contacted with the culture medium, the detection article is contacted with the culture medium to detect Listeria monocytogenes.

Abstract: The present disclosure describes methods for concentrating microorganisms with concentration agents in a sampling device and the sampling device described herein. More specifically, methods for concentrating microorganisms from large volume samples with concentration agents in a sampling device can provide for rapid, low cost, simple (involving no complex equipment or procedures), and/or effective processes under a variety of conditions.

Abstract: An apparatus for processing a sample using microwaves comprises: a reaction vessel comprising a chamber which accommodates a refrigerant and a sample and an injection port through which a gas is injected; a microwave source which irradiates microwaves into the chamber; a connector which carries the gas injected through the injection port; and a gas supplier which is located in the chamber and injects the gas carried by the connector to a refrigerant in the chamber. The connector may comprise a gas carrying portion located above the level of the refrigerant in the chamber.

Abstract: The invention pertains to a novel cell line, an HIV tat-rev dependent GFP-Gaussia luciferase Reporter cell line, known henceforth as the GGR cell line, that detects pseudotype and replication competent HIV (cloned or uncloned isolates, in cell media or human serum) rapidly and with high sensitivity. This GGR cell line provides an improved method of characterizing the entry phenotype of HIV envelope genes, and detecting and examining primary HIV samples in the context of laboratory research, clinical trial monitoring, and medical diagnostics. Examples include, but are not limited to, determining the functional HIV viral load, responsiveness to treatment, characterization of viral co-receptor usage (testing for viral co-receptor usage, i.e., CCR5 vs CXCR4, as required prior to prescribing FDA-approved CCR5 inhibitors), and characterization of other viral or drug resistance phenotypic properties to guide treatment.