Abstract: Methods of the invention involve determining a patient's compliance with a cholesterol lowering therapy. In certain aspects, the invention provides methods that involve conducting a first assay to determine a cholesterol biomarker level in a first sample from a patient prior to the patient undergoing a cholesterol lowering therapy. The methods may also involve conducting a second assay to determine a cholesterol level in a second sample obtained from the patient after the patient has started undergoing a cholesterol lowering therapy. Additionally, the methods involve associating the cholesterol level and the cholesterol biomarker level in which the association allows for the determination of the patient's compliance with the cholesterol lowering therapy.

Abstract: An object of the present invention is to provide a novel glucose dehydrogenase, a method for producing the glucose dehydrogenase, and applications of the glucose dehydrogenase. The flavin-binding glucose dehydrogenase of the invention has the following characteristics (1) and (4): (1) Molecular weight: the molecular weight of a polypeptide moiety in the enzyme is about 68 kDa as measured by SDS-polyacrylamide electrophoresis; (2) Km value: the Km value for D-glucose is about 15 mM or less; (3) Temperature stability: stable at a temperature of 55° C. or less; and (4) pH stability: stable at a pH range of 3.0 to 8.5.

Abstract: Disclosed herein are a gene (polynucleotide) encoding an FAD-conjugated glucose dehydrogenase which can be characterized by reactivity to glucose, thermal stability, substrate-recognition performance, and low activity for maltose; a process for the production of the enzyme using a transformant cell transfected with the gene; a method for the determination of glucose; a reagent composition for use in the determination of glucose; and a biosensor for use in the determination of glucose. An embodiment is a polynucleotide encoding an FAD-conjugated glucose dehydrogenase, comprising a polypeptide whose amino acid sequence comprises X1-X2-X3-X4-X5-X6, wherein X1 and X2 independently represent an aliphatic amino acid residue; X3 and X6 independently represent a branched amino acid residue; and X4 and X5 independently represent a heterocyclic amino acid residue or an aromatic amino acid residue.

Abstract: The present invention provides fusion proteins as biomarkers specific for chromosomal translocation-based conditions (e.g., cancer), related methods for detecting fusion protein biomarkers associated with chromosomal translocation-based conditions, related methods for quantifying amount of fusion protein expression, and related methods for diagnosing chromosomal translocation-based conditions through detection of such fusion protein biomarkers. Such fusion protein biomarkers and related methods additionally find use in research settings.

Abstract: A method for sorting pluripotent cells using a compound which is eliminated from the pluripotent cells through the MDR1 transporter.

Abstract: The present invention pertains to a method of detection, by mass spectrometry, of at least one marker of at least one mechanism of resistance to at least one antimicrobial, resistance of at least one microorganism contained in a sample, characterised in that the antimicrobial is a carbapenem, and said resistance markers are proteins or peptides. Preferably, said proteins or peptides are proteins from said microorganism.

Abstract: Materials and Methods for identifying and measuring pharmacodynamic biomarkers of neuropsychiatric disease (e.g., major depressive disorder), stratifying disease severity, and monitoring a subject's response to treatment are provided.

Abstract: The present invention provides methods for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. The present invention also provides compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g., malignant versus benign, SCLC versus NSCLC).

Abstract: Some embodiments comprise a sample dispersion system including a sample container having a housing with two or more orifices to control the introduction of said fluid and/or the passage of carrier solution into the sample container and/or the passage of fluid from the sample container. The carrier fluid may be moving in a flow from an inlet orifice to an outlet orifice in order to disperse the sample fluid in flow. The sample container may be configured to rotate about an axis substantially parallel to the fluid flow. The sample container may be configured to rotate (or tilt) about an axis substantially perpendicular to the fluid flow. The sample container may alternate from a first position to a second position at controllable rate, frequency, and/or direction.

Abstract: Hydroxyphenylbenzazole compounds that are useful for the selective detection of zinc, aluminum, chromium, and iron cations in vitro and in vivo.

Abstract: The present invention relates to methods and compositions for detecting immune system activation and/or the presence of an immune disorder in a patient. More particularly, methods and compositions for detecting immune system activation and/or the presence of an immune disorder in a patient by detecting, for example, the concentration of certain metabolites of 13C-labeled glutamine, 13C-labeled palmitate, and/or 13C-labeled glucose.

Abstract: A universal data-mining platform capable of analyzing mass spectrometry (MS) serum proteomic profiles and/or gene array data to produce biologically meaningful classification; i.e., group together biologically related specimens into clades. This platform utilizes the principles of phylogenetics, such as parsimony, to reveal susceptibility to cancer development (or other physiological or pathophysiological conditions), diagnosis and typing of cancer, identifying stages of cancer, as well as post-treatment evaluation. To place specimens into their corresponding clade(s), the invention utilizes two algorithms: a new data-mining parsing algorithm, and a publicly available phylogenetic algorithm (MIX). By outgroup comparison (i.e.

Abstract: A neural network is disclosed. The neural network comprises a plurality of optogenetically modified neural cells being three-dimensionally distributed in a hydrogel medium and being disconnected from any solid support having a shear modulus above 1 GPa.

Abstract: A system and method for distributing and agitating an amount of a liquid over a microscope slide, wherein a distribution plate having a microtextured lower surface and at least one passage extending through the plate is secured at a predetermined distance of 10-250 ?m above the microscope slide. Liquid passes through the passage in the distribution plate, and the distribution plate is transversely reciprocated relative to the microscope slide in the plane of the lower surface of the distribution plate or the plane of the upper surface of the microscope slide.

Abstract: Sample taking device for extracting a fluid sample from a vessel comprising: a cover portion for closing the vessel such that, in use a headspace is defined between the cover portion and fluid held in the vessel, a sampling chamber comprising a sampling inlet and a sampling outlet, a cannula adapted to provide, in use, fluid communication between the fluid held in the vessel and the sampling chamber through the sampling inlet, and ports to operate the device in at least two operating conditions: a sample preparing condition in which a pressure in the headspace is greater than that of the sampling chamber such that fluid flows through the cannula towards the sampling chamber and can be retained therein, and a sample dispensing condition in which fluid retained in the sampling chamber can be delivered through the sampling outlet and fluid remaining inside the cannula can return to the vessel.

Abstract: An apparatus and method are described that achieve independent and simultaneous processing of a plurality of substrate-supported biological samples. In one embodiment, substrate holders arranged in a minor arc are independently moveable between a processing position and an access position, and reagents are delivered to substrates held in the substrate holders through a nozzle plate that moves along the arc of substrate holders. The disclosed apparatus and method are particularly suited for implementation of lean processing of biological samples.

Abstract: A detection instrument determines whether a specimen container (e.g., blood culture bottle) is positive for presence of microbial agent growth therein. When the container is deemed positive it is made available (e.g, transferred or exposed to) to an automated instrument performing identification and/or characterization of the microbial agent. The identification and/or characterization instrument removes a portion of the sample from the specimen container and places it into a disposable separation and concentration device. The microbial agent is concentrated via optional selective lysis of non-microbial agent cellular material which may be present and centrifugation. A reading module reads the concentrated microbial agent using spectroscopic methods, e.g., measurements of intrinsic fluorescence. Such interrogation may occur while the microbial agent remains concentrated in the disposable device.

Abstract: A composition is provided for detecting a Salmonella microorganism in sample. The composition comprises at least one first selective agent that inhibits the growth of Gram-positive microorganisms, a first differential indicator system comprising at least one first differential indicator compound that is converted to a first detectable product by a Salmonella microorganism, and a second differential indicator system comprising a second differential indicator compound that is converted by urease enzyme activity to a second detectable product. Optionally, the composition may comprise a third differential indicator system comprising a third differential indicator compound that is converted by a ?-galactosidase enzyme activity to a third detectable product. Methods of using the composition to detect a Salmonella microorganism are also provided.

Abstract: The present invention relates to host cells transformed with a nucleic acid sequence encoding a eukaryotic xylose isomerase obtainable from an anaerobic fungus. When expressed, the sequence encoding the xylose isomerase confers to the host cell the ability to convert xylose to xylulose which may be further metabolized by the host cell. Thus, the host cell is capable of growth on xylose as carbon source. The host cell preferably is a eukaryotic microorganism such as a yeast or a filamentous fungus. The invention further relates to processes for the production of fermentation products such as ethanol, in which a host cell of the invention uses xylose for growth and for the production of the fermentation product. The invention further relates to nucleic acid sequences encoding eukaryotic xylose isomerases and xylulose kinases as obtainable from anaerobic fungi.

Abstract: The efficient production of ethanol from low-cost biomass (e.g., corn, sugar beets, sugar cane, switchgrass and/or paper) has become increasingly important in making ethanol competitive with gasoline and decreasing the United States' dependence on foreign oil. For example, to reduce the cost of transporting biomass to ethanol production facilities, mobile systems for producing ethanol from biomass are provided. Also provided are small-scale ethanol production facilities. For example, instead of transporting biomass to the production facility, the facility is transported to the biomass or is located nearby the source of the biomass. The ethanol production facilities or components thereof may be transported via land, water, or air. Production of other products, such as hydrocarbons, natural gas, hydrogen gas, plastics, polymers, and proteins, can also be made by the methods and facilities. Any product described herein can be made in finished form or un-finished form and moved, e.g., to a fixed facility, e.g.

Abstract: The present invention is a Kluyveromyces lactis yeast strain comprising the sequence identified by SEQ ID NO: 1, and methods for the production of sugars (glucose and galactose), ethanol, ?-galactosidase and biomass, in which said Kluyveromyces lactis yeast strain is cultured in the presence of a lactose-containing medium. The lactose-containing medium may be milk, whey, whey resulting from the preparation of butter, whey resulting after casein precipitation, milk permeate, whey permeate, acid whey and YPL culture medium.

Abstract: The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Abstract: Described herein are methods and materials for reducing degradation of recombinant proteins in fungal cells such as Yarrowia.

Abstract: The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The invention relates to an adenoviral-based biological delivery and expression system for use in the treatment or prevention of osteoathritis in human or mammalian joints by long-term inducible gene expression of human or mammalian interleukin-1 receptor antagonist (Il-1Ra) in synovial cells, comprising a helper-dependent adenoviral vector containing a nucleic acid sequence encoding for human or mammalian interleukin-1 receptor antagonist (Il-1Ra), left and right inverted terminal repeats (L ITR and R ITR), the adenoviral packaging signal and non-viral, non-coding stuffer nucleic acid sequences, wherein the expression of the human or mammalian interleukin-1 receptor antagonist (Il-1Ra) gene within synovial cells is regulated by an inflammation-inducible promoter.

Abstract: Methods and systems for producing a biofuel using genetically modified sulfur-oxidizing and iron-reducing bacteria (SOIRB) are disclosed. In some embodiments, the methods include the following: providing a SOIRB that have been genetically modified to include a particular metabolic pathway to enable them to generate a biofuel; feeding a first source of ferric iron to the SOIRB; feeding sulfur, water, and carbon dioxide to the SOIRB; producing at least the first particular biofuel, a first source of ferrous iron, sulfate, excess ferric iron, and an SOIRB biomass; electrochemically reducing the excess ferric iron to a second source of ferrous iron; providing an iron-oxidizing bacteria that have been genetically modified to include a particular metabolic pathway to enable them to generate a second biofuel; producing at least the second biofuel, a second source of ferric iron, and an IOB biomass; and feeding the second source of ferric iron to the SOIRB.

Abstract: The present invention provides a novel leech HAase and a method of producing low-molecular-weight HA oligosaccharides using the leech HAase. This invention successfully cloned the first leech HAase gene and provides a method for high-level expression of the leech HAase gene. By controlling the incubation condition, different HA oligosaccharides, particularly HA4, HA6, HA8 and HA10, can be selectively generated using the leech HAase. The large-scale expression of the leech HAase and the enzymatic production of specific HA oligosaccharides are not only useful for the cosmetic, healthcare and the medical industries but also can be a great help to polysaccharides chemical synthesis and cancer research.

Abstract: Provided herein are methods for generation and amplification of a single-stranded DNA circle in a single reaction vessel from a linear DNA without any intervening purification steps. The single-stranded DNA circle is generated via a template-independent single-stranded DNA ligation. Whole-genome amplification of circulating nucleic acids extracted from blood is provided. Kits for performing the disclosed methods are also provided.

Abstract: The invention provides an ultra-rapid nucleic acid amplification method performed in a flow channel. Specifically, the invention provides a nucleic acid amplification method for performing a PCR reaction by supplying a PCR sample solution to a nucleic acid amplification device comprising a serpentine channel adapted to perform at least one PCR cycle, the nucleic acid amplification device comprising a DNA denaturation temperature zone corresponding to the curved portions at one side, an annealing temperature zone corresponding to the curved portions at the other side, and an extension temperature zone positioned between the annealing and DNA denaturation temperature zones, wherein the PCR sample solution is introduced in the form of sample plugs separated by gas into the serpentine channel using a pump, the sample solution being supplied into the channel in a state such that the solution is separated by gas into a segment corresponding to one PCR cycle or smaller segments.

Abstract: Provided is a chip process of gene synthesis, and the process comprises incorporating the whole procedure, which comprises amplifying oligonucleotides and assembling the oligonucleotides into a gene in parallel, onto a single chip. A specific mismatch endonuclease is also used in the process to establish an error repair system in gene synthesis, and the error rate is decreased to about 0.19 mismatched bases/kb. The high-throughput, high-fidelity and low-cost chip process of gene synthesis provided in the present invention can meet the requirements of gene synthesis and the optimization and screening of protein expression on a large scale at the frontier of life sciences such as synthetic biology, genomics, and systems biology.

Abstract: This disclosure provides, among other things, a method of combining nucleic acid fragments, comprising: (a) providing two double-stranded DNA molecules with a common sequence, wherein the common sequence is at the end of each molecule; (b) nicking one strand in the common sequence of both molecules at a respective nicked site; (c) moderately denaturing both molecules to remove a single-stranded fragment from the nicked site to one end of each molecule, wherein the single-stranded fragment includes the common sequence in part or in whole, resulting in an overhanging sequence in each molecule, and the overhanging sequences in both molecules are complementary to each other; (d) allowing the overhanging sequences of both molecules to anneal to each other, and ligating the molecules. Alternative ways for performing the method are also provided.

Abstract: Disclosed herein are compositions and methods for generating chromosomal translocations and targeted deletions of specific lengths and at specific locations the genome of cell.

Abstract: The present invention provides isolated polypeptides having alpha-amylase activity catalytic domains, carbohydrate binding domains and polynucleotide encoding the polypeptides, catalytic domains or carbohydrate binding domains. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or carbohydrate binding domains.

Abstract: A method for pretreating lignocellulosic biomass by: a) acid hydrolysis with an acid solution resulting in a liquid fraction and a solid fraction, b) separating the solid fraction and the liquid fraction, c) drying the solid fraction, d) firing the dried solid fraction in a medium comprising at least one hydrated inorganic salt to obtain a solid fraction and a liquid fraction, e) separating the solid fraction and the liquid fraction obtained in d), f) optionally, treating said solid fraction obtained in e), g) enzymatic hydrolysis of said solid fraction obtained in e) and/or f), and wherein at least a portion of the liquid fraction obtained in b) is used to grow microorganisms which produce the enzymes necessary for the enzymatic hydrolysis of g).

Abstract: To produce quinolinate effectively, a L-aspartate oxidase variant that the feedback regulation by nicotinic acid or NAD is released, and a microorganism including the L-aspartate oxidase variant are provided. Quinolinate may be effectively produced by culturing of the microorganism including the L-aspartate oxidase variant.

Abstract: The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds. The engineered ketoreductase polypeptides are optimized for catalyzing the conversion of N-methyl-3-keto-3-(2-thienyl)-1-propanamine to (S)—N-methyl-3-hydroxy-3-(2-thienyl)-1-propanamine.

Abstract: The disclosure relates to engineered enone reductase polypeptides having improved properties, polynucleotides encoding the engineered polypeptides, related vectors, host cells, and methods for making the engineered enone reductase polypeptides. The disclosure also provides methods of using the engineered enone reductase polypeptides for chemical transformations.

Abstract: Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding multizymes (i.e., single polypeptides having at least two independent and separable enzymatic activities) along with a method of making long-chain polyunsaturated fatty acids (PUFAs) using these multizymes in plants and oleaginous yeast are disclosed.

Abstract: The present invention improves biodiesel production in several ways. Unique combinations of unit operations and flow configurations are disclosed in mobile processing units that are feedstock-flexible and can be dynamically deployed in a distributed way. In some embodiments, a process includes introducing a waste oil and an alcohol into a reactor with an esterification-transesterification enzymatic catalyst. Free fatty acids are reacted with alcohol to produce fatty acid alkyl esters, and glycerides are reacted with alcohol to produce fatty acid alkyl esters and glycerin. A membrane separator removes glycerin, water, and alcohol. Unreacted free fatty acids are then separated and recycled, to generate a product stream with fatty acid alkyl esters. A genset may be provided for combusting glycerin to produce electrical power and thermal heat as co-products. This biodiesel process may be energy self-sufficient, require no external utilities, and avoid direct discharge of wastewater.

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 propiony-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: A reactor system is provided for improved fermentation of a gaseous substrate through the introduction of a secondary loop to a forced-circulation loop reactor. The reactor comprises a primary loop through which fermentation broth comprising a gaseous substrate is circulated through a riser segment and a downcomer section by a loop pump. Downstream of the loop pump a portion of fermentation broth is withdrawn from the downcomer section and is directed to the top of the reactor via a secondary loop. Further provided is a method for improving the mass transfer of a gaseous substrate to a fermentation broth in a fermentation vessel comprising a secondary loop. Further provided is a method for reducing foam in the headspace of a fermentation vessel comprising a secondary loop.

Abstract: Embodiments of the present invention concerns methods and compositions for the construction of a series of vectors containing a chemical sensing module to assess the production of a chemical compound by a microorganism.

Abstract: A genetically engineered bacterial cell wherein activity of a pathway in the cell of converting ?-ketoglutarate into succinate semialdehyde; or activity of succinyl semialdehyde dehydrogenase in the cell is increased compared to the activity in a non-genetically engineered cell of the same type, and a method of producing succinic acid by using the same.

Abstract: The invention relates generally to methods and compositions for maintaining and manipulating microbial cultures of Gram-positive bacteria. Also provided are methods for identifying quorum sensing regulatory proteins and auto-inducing peptides in Gram-positive bacteria. Also provided are methods and compositions believed to affect quorum sensing pathways of the genus Clostridium to direct or maintain enhanced butanol production of Clostridium in a desired differentiated state during sequential or continuous culture. Differentiated states include extended serial propagation, and continuous culture, for the production of butanol or other fermentation products. Further provided are methods where the concentration of butanol in peptide treated cultures of the genus Clostridium increase more rapidly and produce a substantially greater amount of butanol than in Clostridium cultures not treated with the peptide.

Abstract: The promoter of the present invention causes a desired gene to be highly expressed, especially in thermotolerant yeast. The promoter is located upstream of the PIR1 gene or the CTR1 gene on the Kluyveromyces marxianus chromosome and comprises a region controlling expression of the PIR1 gene or the CTR1 gene.

Abstract: A system for generating biogas comprises at least one fermenter (1) for fermenting solid biomass (13). The fermenter (1) comprises a device for charging the biomass with a liquid medium, a gas outlet (2) for removing the biogas from the fermenter (1) and a gas inlet (3) for supplying gases to the fermenter (1). The gas inlet (3) is connectable to a biogas source, preferably to the gas outlet (2), a biogas line and/or a biogas reservoir.

Abstract: The invention provides improved methods for the production of isoprene from biological materials.

Abstract: The present invention provides compounds, pharmaceutically acceptable compositions thereof, and methods of using the same.

Abstract: The present invention provides methods for improving the specificity of nucleic acid amplification comprising incubating a nucleic acid molecule with a polymerase-Sso7 DNA binding domain conjugate and arginine, spermidine, or spermine. The present invention also provides reaction mixtures and kits for improving the specificity of nucleic acid amplification.