Abstract: The invention relates to recombinant microorganisms that have been engineered to produce various chemicals using genes that have been repurposed to create a reverse beta oxidation pathway. Generally speaking, the beta oxidation cycle is expressed and driven in reverse by modifying various regulation points for as many cycles as needed, and then the CoA thioester intermediates are converted to useful products by the action of termination enzymes.

Abstract: This invention discloses a constitutive promoter for expression of foreign or endogenous coding sequences in plants, including dicotyledonous and monocotyledonous plants. The invention also discloses a chimeric nucleic acid construct comprising the promoter of the invention operably linked to a foreign or endogenous polynucleotide that codes for a protein of interest or a transcript capable of modulating expression of a target gene. The invention further discloses transformed plant cells, as well as differentiated plants and plant parts, containing the construct. Methods for diagnosis and treatment of viral infections, especially badnaviral infections, are also disclosed.

Abstract: The invention provides isolated maize EIN3, EBF1 and EIN5 nucleic acids and encoded proteins which are associated with ethylene signaling in plants. The present invention provides methods and compositions relating to altering ethylene sensitivity in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants and antibody compositions.

Abstract: The present invention relates to transgenic plants that have increased nitrogen use efficiency, stress tolerance, or both and that have been transformed using a novel vector construct including nucleic acid sequences that modulate nitrogen use in plants. In various embodiments, the vector construct includes one or more nucleic acid sequences selected from the group consisting of SEQ ID NO: 2, 4, 7, 9, 11, 13, 15, 17, 22, 24, 26, 28, 30, 32, 34, 36, or 38. The invention also relates to isolated vectors for transforming plants and to antibodies used for detecting transformed plants. The invention also relates to methods of expressing in plants the nucleic acid molecules corresponding to the nucleic acid sequences that modulate nitrogen use in plants or are modulated by nitrogen conditions.

Abstract: The invention relates to novel nucleic acids and their encoded polypeptides from ASR and methods of use that enhance the plant's defensive elicitation response.

Abstract: The present disclosure provides methods and compositions to selectively modulate RNA processing. The methods and compositions selectively enhance or repress RNA processing by up- or down-regulating Drosha expression and/or by providing RNA sequences with mis-matches introduced or removed 5 and/or 9-12 nucleotide positions from the Drosha cutting site. Therapeutic uses of the methods and compositions are also described.

Abstract: The immune response to an antigen of interest, especially one in purified form, can be significantly enhanced by the simultaneous administration of an alphavirus replicon particle which expresses the same antigen. This allows for the use of significantly smaller quantities of the protein antigen than in conventional immunization strategies, and this new immunization strategy can also eliminate the need for boosting administration of the antigen or it can reduce the number of boosts required for an effective immune response to the antigen.

Abstract: Attenuated, replication-deficient viruses such as vaccinia viruses are used to deliver an exogenous viral, bacterial, parastic or tumor antigen to an epidermal tissue such as the skin, lungs or gastrointestinal tract, which has been mechanically disrupted, in an amount effective to elicit or stimulate a cell mediated immune response. The epidermis may be mechanically disrupted prior to, at the same time, or immediately after the administration of the vaccine. The vaccine can be used to induce immunity against a pathogen, such as a virus, bacteria, or parasite, or against a cancer in a subject that has or is at risk of developing cancer.

Abstract: A process and apparatus for the anaerobic digestion of organic wastes, preferably to also produce a useful biogas, is described. The waste may have a total solids (TS) concentration of 6% or less while a digester is operated at a higher solids concentration, for example with a feed TS concentration of 8-12%. One or more separation stages downstream of the digester separate active bacteria and undigested organics from the digestate, and return separated matter to the digester. Optionally, a feed thickening apparatus and step may be provided upstream of the digester. The upstream thickener and recycle from the downstream separation stages are operated such that the TS of the combined inputs to the digester is within a desired range.

Abstract: A process for the production of biogas from biodegradable material is disclosed, the process comprising the steps of: (a) adding the biodegradable material to the reactor; (b) inoculating a microorganism; (c) adding a colloidal solution of surface-modified iron oxide nanoparticles to the reactor; (d) providing anaerobic conditions; (e) carrying out an anaerobic digestion; and (f) collecting the biogas; wherein the steps (a), (b) and (c) can be carried out in any order.

Abstract: A method for the treatment of lignocellulose-containing materials wherein such lignocellulose-containing materials, normally resistant to biotreatment, are first subjected to pyrolysis to produce pyrolysis products including pyrogas and char. Exemplary applications of the method include pyrolytic pre-treatment of wastewater sludges, cellulosic wastes, wood, peat, plant residues, low-grade coal, and the like. The pyrogas is introduced into digester sludge in an anaerobic digester.

Abstract: A process for the use of peracid compositions to eliminate and/or control the growth of undesirable bacteria, including contaminating bacteria, in the fermentation production of alcohol is disclosed. Beneficially, the peracid compositions and methods of use of the same do not interfere or inhibit the growth or replication of yeast and have low or no adverse environmental impact.

Abstract: A system and method for managing an ethanologen for use in biorefinery is disclosed. The method for propagating ethanologen for use in the production of a fermentation product from biomass comprises the steps of providing a medium for propagation of ethanologen and supplying a first cell mass of ethanologen to the medium. A first cell mass of ethanologen is propagated into a larger second cell mass of ethanologen.

Abstract: A method to increase ethanol production from a corn dry-mill process is described that comprises adding an enzyme preparation derived from Trichoderma reesei having cellulolytic activity to a saccharification process that includes conventional alpha amylase and glucoamylase. The addition of the cellulolytic enzyme decreases viscosity of the saccharified mash and can increase ethanol yield from a dry grind fermentation by as much as 10% or more. Specific characteristics are provided to show surprising and advantageous results of one particular preparation of cellulolytic enzymes from T. reesei.

Abstract: Provided herein are metabolically-modified microorganisms useful for producing biofuels. More specifically, provided herein are methods of producing high alcohols including isobutanol, 1-butanol, 1-propanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 2-phenylethanol from a suitable substrate.

Abstract: A recombinantly modified Corynebacterium glutamicum microorganism with an improved 1,4-butanediol (1,4-BDO) productivity relative to an unmodified Corynebacterium glutamicum microorganism, wherein activity of an enzyme catalyzing a conversion reaction between malate and oxaloacetate is inactivated or reduced relative to an unmodified Corynebacterium glutamicum microorganism, as well as a method of making and using same.

Abstract: A yeast cell comprising LDH from a Sordaria genus fungi, in which activity of lactate dehydrogenase converting pyruvate into lactate is increased, as well as a method of preparing the yeast cell and a method of using the yeast cell to produce lactate.

Abstract: Provided is a mutant of propionyl-CoA transferase from Clostridium propionicum that can convert lactate into lactyl-CoA with high efficiency in a method of preparing a polylactate (PLA) or PLA copolymer using microorganisms. Unlike conventional propionyl-CoA transferase which is weakly expressed in E. coli, when a mutant of propionyl-CoA transferase from Clostridium propionicum is introduced into recombinant E. coli, lactyl-CoA can be supplied very smoothly, thereby enabling highly efficient preparation of polylactate (PLA) and PLA copolymer.

Abstract: Acyl-CoA:lysophosphatidylcholine acyltransferase [“LPCAT”] having the ability to convert acyl-CoA+1-acyl-sn-glycero-3-phosphocholine to CoA+1,2-diacyl-sn-glycero-3-phosphocholine (EC 2.3.1.23) is disclosed herein to be over-expressed along with the over-expression of phospholipid:diacylglycerol acyltransferase [“PDAT”] having the ability to transfer a fatty acyl group from the sn-2 position of a phospholipid (e.g., phosphatidylcholine) to the sn-3 position of 1,2-diacylglycerol [E.C.2.3.1.158], thus resulting in a lysophospholipid and TAG. Co-expression of these enzymes in a recombinant microbial host cell resulted in increased production of long chain polyunsaturated fatty acids [“PUFAs”].

Abstract: Methods for enhancing a biological activity, for example, catalytic activity, of a lipase, are provided. In some embodiments, the methods include the step of alkylating one or more cysteine residues present within the lipase. Also provided are modified polypeptides for which a biological activity is enhanced by the disclosed methods, methods for using the disclosed polypeptides, including for the transesterification of renewable oils to produce a biofuel, and cell free systems that include a lipase, to which one or more moieties, such as steroidal moieties, are conjugated.

Abstract: The present invention relates to methods of degrading or converting biomass material enriched with hemicellulosic material into fermentable sugars.

Abstract: The invention relates to a method for the production of adenosine 3?,5?-monophosphate (cAMP) by a permeable microbial strain which uses polyols for protecting activities of enzymes and a cAMP precursor and phosphate as substrates. Glucose is used as an energy provider and metal ions and an organic solvent such as acetone are used in the medium.

Abstract: A cDNA synthesis method includes: mixing a lysis solution containing a chaotropic substance and a nucleic acid-binding solid-phase carrier in a sample containing a ribonucleic acid (RNA), thereby adsorbing the RNA on the carrier; reverse-transcribing the RNA adsorbed on the carrier while keeping the RNA adsorbed on the carrier in a reverse transcription reaction mixture, thereby synthesizing cDNA; and eluting the synthesized cDNA with an eluent.

Abstract: Methods and compositions for the amplification of nucleic acids are disclosed. Amplification methods provided herein may be performed under isothermal conditions. Methods and compositions may include reagents such as restriction enzymes, polymerases, ligases, primers, and polynucleotide adaptors.

Abstract: The present invention relates to a method for producing natively folded disulfide bond containing proteins in a prokaryotic host. The method comprises that in the cytoplasm of a prokaryotic cell is expressed protein(s) of interest that naturally contain disulfide bonds and naturally occurring or inverted transmembrane enzyme, wherein the cysteines of the active site(s) are naturally or after genetic engineering located towards the prokaryotic cytoplasm. The enzyme is selected from the group of VKOR, inverted VKOR (iVKOR) and inverted Dsb B (iDsb B). In the prokaryotic cell is also expressed cytoplasmic DsbA or a corresponding protein being capable of providing electrons to the active site(s) of VKOR, iVKOR or iDsbB. The invention relates also to a prokaryotic host cell and a vector system for producing natively folded disulfide bond containing proteins.

Abstract: Disclosed are methods for reducing detectable mannosylation of N-linked and O-linked oligosaccharides in lower eukaryote host cells. In particular, recombinant lower eukaryote host cells are provided in which expression of the GDP-mannose transporter encoded by the Vanadate Resistant Glycosylation 4 (VRG4) gene has been disrupted. In general, the VRG4 gene is essential for cell viability; however, the present invention provides host cells that are viable when expression of the VRG4 gene therein has been disrupted. The host cells are capable of producing proteins or glycoproteins that have reduced or no detectable ?-linked mannose, ?-linked mannose or phosphomannose containing N- and/or O-glycans.

Abstract: This invention describes methods for detecting target analytes by utilizing an electroactive moiety (EAM) that functions as a substrate for a specific enzyme. If target analyte is present, a functional group is enzymatically removed from a transition metal complex resulting in quantifiable electrochemical signal at two unique potentials, E01 and E02 that is detected through a self-assembled monolayer (SAM) on an electrode.

Abstract: A process for preparing information that identifies a compound as capable of perturbing the epithelium in a D. melanogaster comprising the steps of: i) obtaining a D. melanogaster which is genetically unmodified except that the D. melanogaster optionally comprises at least one nucleotide sequence encoding a reporter polypeptide operably linked to a promoter of an endogenous protein; ii) contacting the D. melanogaster with the compound; and iii) determining whether there is a difference between the epithelium of the D. melanogaster of ii) and the epithelium of a corresponding D. melanogaster not contacted with the compound, wherein the presence of a difference between the epithelium of the D. melanogaster contacted with the compound and the epithelium of a corresponding D. melanogaster not contacted with the compound identifies the compound as a compound that is capable of perturbing the epithelium in a D. melanogaster.

Abstract: The present invention pertains to a method for in vitro diagnosing a bacterial infection in a biological fluid selected amongst cerebrospinal fluid, ascitic fluid, pericardial fluid, pleural fluid, urine and synovial fluid, based on the measure, in a sample of said fluid, of the production of reactive oxygen species (ROS); a high level of ROS production is indicative of the presence of activated polymorphonuclear neutrophils (PMNs) in said fluid, which in turn is a hallmark of bacterial infection.

Abstract: This invention relates to a biological indicator derived from a composition comprising: a host organism comprising a spore forming bacteria; a reporter gene for producing an indicator enzyme; a regulatory gene; and a vehicle for inserting the reporter gene and the regulatory gene in the host organism; the host organism bearing a transposable genetic element in its genome for inserting an insertion sequence in the regulatory gene; the insertion sequence comprising a transposase, a pair of terminal inverted repeat sequences, and at least one open reading frame for expressing the transposase. The vehicle may be taken up by the host organism. The insertion sequence may be inserted in the regulatory gene. The host organism may undergo sporulation to form the biological indicator. A process and an apparatus for using the biological indicator are disclosed.

Abstract: Methods for separating pericarp tissue from surrounding tissues in grain are provided. Included are methods for isolation of high-purity pericarp DNA from a grain plant that reflects the genotype of the maternal parent of the grain plant, such that the isolated DNA may be used in a PCR-based genotyping assay.

Abstract: Provided herein are methods for detecting an Aspergillus protease in a sample, diagnosing a subject with aspergillosis caused by an Aspergillus infection based on the presence of an Aspergillus protease in a sample, and methods of aspergillosis treatment that incorporate these diagnostic methods. In certain embodiments, the Aspergillus protease is Asp f2, and the Aspergillus infection is caused A. fumigatus, A. flavus, A. versicolor, A. niger, or A. terreus. Also provided herein are antibodies and kits for use in these methods, including novel antibodies specific for Asp f2.

Abstract: A biological process indicator is provided for validating a treatment process in which the amount or activity of a contaminant in a sample is reduced. The indicator comprises a thermostable kinase covalently linked to a biological component, with the proviso that the biological component is not an antibody. Methods of preparing the indicator, and methods of using the indicator, are also provided.

Abstract: Reagent materials and associated test elements are provided. In one embodiment, a test element having dual functionality includes a first coenzyme-dependent enzyme or a substrate for the first enzyme, a second coenzyme-dependent enzyme or a substrate for the second enzyme, and a coenzyme selected from the group consisting of thio-NAD, thio-NADP, and a compound according to formula (I). In one aspect, the first analyte is hydroxybutyrate and the first enzyme is a hydroxybutyrate dehydrogenase, and the second analyte is glucose and the second enzyme is a glucose dehydrogenase or a glucose oxidase. Other aspects of the subject application are directed to unique reagent materials. Further embodiments, forms, objects, features, advantages, aspects, and benefits shall become apparent from the description and drawings.

Abstract: The present invention relates to a method of amplifying a first and a second target nucleic acid in separate reaction receptacles, wherein said reaction receptacles comprise a solution comprising amplification reagents and oligonucleotides specific for said first or said second target nucleic acid, wherein said solution is the same for amplifying said first target nucleic acid and said second target nucleic acid.

Abstract: The invention relates to a method for purification of nucleic acids, to a kit for performing the method according to the invention and to a new application of magnetic particles for purification of a biological sample. The method according to the invention comprises the following steps: a) accommodating of the sample in a first sample vessel in an aqueous solution and lysing of the sample under non-chaotropic conditions; suspending of first magnetic particles in the solution and inserting of the first sample vessel in a sample vessel holder, wherein the sample vessel is inserted in the annular interior space of a ring magnet associated with the sample vessel holder; separating of the solution from the magnetic particles; and isolating of the nucleic acids from the solution.

Abstract: An apparatus and a method for obtaining a (poly)nucleotide sequence of interest include steps of cultivating hosts cells to produce a nucleotide sequence of interest and harvesting these cells, introducing these cells in a passageway and disintegrating them in a continuous process. In the continuous process, performing in the passageway a precipitation of contaminants by a mixing of the disintegrated cells with a solution containing one or more salt(s) and obtaining a mixture and allowing a precipitate to separate from the solution of this mixture, preferably to float and/or to sediment from the solution of this mixture for 1-48 hours and pumping out a soluble material from this solution, while excluding recovering the precipitate.

Abstract: The invention is related to a method and test kits for quantitative determination of polynucleotide amounts present in a sample. The test kit comprises organized pools with polynucleotide probes having distinct sizes and optionally provided with tracer tags or primer tags. The probes are allowed to hybridize with affinity tagged analyte polynucleotides from the sample. The result is hybrids, which can be recovered on a separation aiding tool provided with the pair of the affinity tag. After the quantitative release of the probes, the probes are either directly recorded, or if primer tagged, they are amplified and optionally provided with a tracer tag before recording. The invention provides a sensitive and quantitative determination of the amount polynucleotides present in a cell or tissue sample and allows a quantitative assessment of variations in the amounts of polynucleotides as a response to inherent changes or due to external stimuli.

Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.

Abstract: A method of detecting a target nucleic acid by sandwich hybridization using a detection probe that hybridizes with the target nucleic acid, and a capture probe immobilized on a support wherein at least one nucleic acid base in the nucleic acid molecule(s) of the detection probe and/or capture probe with a photoreactive group includes irradiating, with light, a complex formed by hybridization between the target nucleic acid and the detection probe and/or capture probe to allow formation of a covalent bond(s) between the photoreactive group(s) and a nucleic acid base(s) in the target nucleic acid.

Abstract: Methods are provided for diagnosing in a subject a condition, such as a carcinoma, sarcoma or leukemia, associated with hypermethylation of genes by isolating the genes from tissue containing as few as 50 to 1000 tumor cells. Using quantitative multiplex methylation specific PCR (QM-MSP), multiple genes can be quantitatively evaluated from samples usually yielding sufficient DNA for analyses of only 1 or 2 genes. DNA sequences isolated from the sample are simultaneously co-amplified in an initial multiplex round of PCR, and the methylation status of individual hypermethylation-prone gene promoter sequences is then determined separately or in multiplex using a real time PCR round that is methylation status-specific. Within genes of the panel, the level of promoter hypermethylation as well as the incidence of promoter hypermethylation can be determined and the level of genes in the panel can be scored cumulatively. The QM-MSP method is adaptable for high throughput automated technology.

Abstract: The present disclosure provides novel primers and method for the detection of specific nucleic acid sequences. The primers and methods provided herein are useful in a wide variety of molecular biology applications and are particularly useful in allele-specific PCR.

Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting under primer extension conditions a genomic sample comprising a test genome with a set of at least ten sequence-specific primers that are complementary to sites in only one strand of a reference chromosomal region, to produce primer extension products, and b) analyzing the primer extension products to identify a chromosomal rearrangement in the test genome.

Abstract: The present invention relates to maintaining the activity and stability of enzymes and biologically active proteins at increased temperatures by contacting same with a combination of isolated passive and active chaperones from a hyperthermopilic Archaeon, wherein the chaperones may include heat shock proteins, prefoldin and/or chaperonin proteins.

Abstract: The present invention provides systems, methods, and compositions for performing molecular tests. In particular, the present invention provides methods, compositions and systems for generating target sequence-linked solid supports (e.g., beads) using a solid support linked to a plurality of capture sequences and capture primers composed of a 3? target-specific portion and a 5? capture sequence portion. In certain embodiments, the target sequence linked solid support is used in sequencing methods (e.g., pyrosequencing, zero-mode waveguide type sequencing, nanopore sequencing, etc.) to determine the sequence of the target sequence (e.g., in order to detect the identity of a target nucleic acid in sample).

Abstract: The present invention is related to an improved method for HER2 gene test by using quantitative real-time PCR (Polymerase Chain Reaction) technique. Our invention streamlines test process, and incorporates quality control for each major step, including sample, reagent, operation, and data report. We eliminate the need for reference genes which is hard to standardize in HER2 PCR test. We develop a cutoff reference point by using the statistical mean of tumor tissue population, and adopt a simplified scoring scheme for evaluation of HER2 status. Our invention produces consistent result across machines and labs, and has proven to be clinically successful in HER2 test.

Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.

Abstract: The invention provides novel nucleic acid polymerases from strains GK24 and RQ-1 of Thermus thermophilus, and nucleic acids encoding those polymerases, as well as methods for using the polymerases and nucleic acids.

Abstract: A method for sequencing a polynucleotide strand by using sequencing-by-synthesis techniques. To address the problem of incomplete extension (IE) and/or carry forward (CF) errors that can occur in sequencing-by-synthesis reactions, an alternative flow ordering of dNTPs is used. In contrast to conventional flow orderings, the dNTPs are flowed in an ordering that is not a continuous repeat of an ordering of the four different dNTPs. This alternate flow ordering may reduce the loss of phasic synchrony in the population of template polynucleotide strands that result from IE and/or CF errors.