Abstract: Provided are methods for detecting, characterizing or separating DNA based on methylation. Heterogeneous DNA populations are separated based on DNA methylation by providing a membrane having a nanopore through which an electric field is applied. DNA of interest is introduced, and for a given threshold voltage across the nanopore, only DNA having a methylation parameter of interest may transit the pore, thereby facilitating detection, characterization, or separation of DNA based on methylation. The methods are optionally used to detect a disease state that is associated with DNA methylation including, but not limited to, cancer.

Abstract: The present teachings provide DNA methylation quantification methods that avoid bisulfite treatment of DNA. Methylation-specific binding proteins (MeDNA binding proteins) and non-methylation specific binding proteins (non-MeDNA binding proteins) are employed in various embodiments to modulate the accessibility of nucleic acids to primer extension reactions. After selectively removing the target nucleic acids, the extension products can be analyzed and methylation quantitated. In some embodiments, the analysis comprises real-time PCR.

Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.

Abstract: The present invention is directed to a panel of single nucleotide polymorphisms (SNPs) in specific genes that serve as biomarkers for sex-specific prenatal loss of a conceptus or embryo. There is provided herein methods and reagents for assessing the specific SNPs in those genes. The method useful in applying these SNPs in predicting an increased risk of prenatal loss is also disclosed.

Abstract: In one aspect, the invention relates to a method for fixing a short nucleic acid in a biological sample. In another aspect, the invention relates to a method for detecting a target short nucleic acid in a biological sample. The method includes contacting the biological sample with an aldehyde-containing fixative, and subsequently contacting the sample with a water-soluble carbodiimide. In a further aspect, the invention relates to a kit for fixing a short nucleic acid in a biological sample. The kit includes a support substrate for holding the sample; an aldehyde-containing fixative; and a water-soluble carbodiimide.

Abstract: The present invention provides methods, kits, and compositions for detecting mutations in transient receptor potential cation channel, subfamily V, member 4 (TRPV4). In particular, mutations are detected in TRPV4 to detect diseases such as scapuloperoneal spinal muscular atrophy (SPSMA) and hereditary motor and sensory neuropathy type IIC (HMSN IIC) or Charcot-Marie-Tooth disease type 2C (CMT2C).

Abstract: Polynucleotide-encoded capture agents for target detection and in particular modular polynucleotide-capture agents comprising a target binding component, a scaffold component and an encoding component formed by standardized molecular units that can be coupled and decoupled in a controlled fashion, and related compositions methods and systems.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.

Abstract: The present invention demonstrates the differential sensitivity of PBLs from lung cancer patients and healthy controls to NNK-induced genetic damage. The data provide convincing evidence that the preferred CBMN assay is a robust test for detection of this sensitivity and yields results that are a good predictor of, for example, lung cancer risk. The simplicity, rapidity, and sensitivity of the CBMN test make it a valuable tool for screening and, for example, prioritizing potential cases for early detection of the disease.

Abstract: The present invention describes compositions for both diagnostic and therapeutic applications. In one embodiment, the present invention contemplates a vaccine formulation comprising an antigen and IL12R?1 isoform 2. In some embodiments, this invention relates to a method of quantifying the ratio of IL12R?1 transcript and a splice variant thereof in a sample, including but not limited to at the cDNA level. In other embodiments, this invention relates to a method of augmenting an immune response by administering, inhibiting and/or inducing IL12R?1 isoform 2.

Abstract: Peptide-lipid constructs of the structure L-S-F are disclosed, where F is a peptide, S is a spacer covalently linking F to L via an oligomer of ethylene glycol, and L is a diacyl- or dialkyl-glycerolipid (including glycerophospholipids). The spacer ideally has 6 to 14 ethylene glycol repeats, corresponding to PEG with a molecular weight of approximately 250 to 600. Also disclosed is a method of detecting reactive antibodies in serum by contacting serum with cells modified to incorporate a peptide-lipid construct, where the peptide is an epitope of the antibody, and determining the degree of aggluthination of the cells.

Abstract: Provided is a lab-on-a-chip. The lab-on-a-chip includes a first region where a lower substrate and an upper substrate are bonded to each other, a second region where the lower and upper substrates are not bonded, and a gap adjusting member disposed at an end of the second region that is opposite to a boundary between the first and second regions, the gap adjusting member being configured to adjust a gap between the first and second substrates to control a capillary force.

Abstract: Antibodies against ?-N-methylamino-L-alanine (“BMAA”) their production, use and related kits; also the immunogens and methods used to obtain the antibodies.

Abstract: The invention relates to a method for detecting endotoxins in a sample.

Abstract: Protein kinases are important signaling molecules involved in tumorigenesis. Mutational analysis of the human tyrosine kinase gene family (98 genes) identified somatic alterations in -20% of colorectal cancers, with the majority of mutations occurring in NTRK3, FES, GUCY2F and a previously uncharacterized tyrosine kinase gene called MCCK/MLK4. Most alterations were in conserved residues affecting key regions of the kinase domain. These data represent a paradigm for the unbiased analysis of signal transducing genes in cancer and provide useful targets for therapeutic intervention.

Abstract: The present invention provides an approach for the simultaneous determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of potentiators of cellular activation allows for characterization of such pathways and cell populations.

Abstract: Compositions, methods and devices for the detection of anti-lipoidal antibodies and the diagnosis of disease, for example, syphilis, are described. In particular, a method for immobilizing a lipoidal antigen, comprising cardiolipin, lecithin, and cholesterol, on a solid support (such as a nitrocellulose membrane) is described. The ability to immobilize a lipoidal antigen on a membrane satisfies a long-felt need for a membrane-based assay for the detection of anti-lipoidal antibodies. Also described are immunoassay devices for concurrently performing treponemal and non-treponemal tests for syphilis.

Abstract: Methods and kits are provided for diagnosing a kidney disease, or the risk thereof, in a subject. The methods include determining an amount of at least one peptide biomarker disclosed herein in a biological sample from the subject and comparing the amount of the at least one peptide in the sample with a control level, wherein if the amount determined is different than the control level, the subject is diagnosed as having, or at an increased risk of developing, the kidney disease.

Abstract: The present invention provides a method comprising allowing a reaction of a sample, a reagent containing Factor C, which can be activated by binding with endotoxin, and a synthetic luminescent substrate comprising a luminescent substrate bound to a peptide, for release of the luminescent substrate from the synthetic luminescent substrate, allowing a luminescent enzyme to act on the luminescent substrate released in the luminescent substrate release step, for measurement of the luminescence intensity, and quantifying the level of endotoxin in the sample based on a measured value obtained in the luminescence measuring step, the method enabling endotoxin to be simply and quickly measured at a level that cannot be detected in conventional methods for endotoxin measurement, without use of any dedicated measuring device.

Abstract: A codon-optimization of nucleic acid for coding apo-clytin-II protein is provided. Luminescent activity of clytin-II is remarkably enhanced. Accordingly, compared with the conventional use of the wild-type clytin-II, an intracellular calcium ion can be detected much more easily.

Abstract: The invention provides methods of producing functional split inteins having small N-intein and/or small C-intein. Using these split inteins with their protein trans-splicing and cleavage activities, we provide new and more effective methods of manipulating proteins. They include site-specific addition of synthetic peptides at protein's terminal and internal locations, ligation of synthetic and/or expressed polypeptides, controllable cyclization of synthetic and/or expressed polypeptides, and controllable cleavages of recombinant proteins. These methods have numerous utilities including but not limited to protein fluorescence labeling, fixation on microchips, site-specific PEGylation, and linkage with pharmaceutical molecules.

Abstract: The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetase that can incorporate the unnatural amino acid phenylselenocysteine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal aminoacyl-tRNA synthetases, polynucleotides encoding the novel sythetases molecules, methods for identifying and making the novel synthetases, methods for producing containing the unnatural amino acid phenylselenocysteine and translation systems. The invention further provides methods for producing modified proteins (e.g., lapidated proteins) through targeted modification of the phenylselenocysteine residue in a protein.

Abstract: A composition comprising neutrophil gelatinase-associated lipocalin (NGAL), which has been enriched from urine, has a molecular weight of about 24.9 kDa to about 25.9 kDa, and comprises a plurality of isoforms having isoelectric points (pIs) ranging from about 5.9 to about 9.1; a composition comprising NGAL, which has been enriched from recombinant Chinese hamster ovary (CHO) cells, has a molecular weight of about 25.9 kDa to about 27.9 kDa, and comprises a plurality of isoforms having pIs ranging from about 5.6 to about 9.

Abstract: Anti-CD22 antibodies and immunoconjugates thereof are provided. Methods of using anti-CD22 antibodies and immunoconjugates thereof are provided.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analysis include nucleic acid amplification and detection and immuno-PCR.

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

Abstract: The present invention provides a method for constructing recombinant translationally coupled operons, a method for producing useful metabolites using the bacterium containing the coupled operons, and a method for monitoring gene expression.

Abstract: A process for the treatment of biomass to render structural carbohydrates more accessible and/or digestible using concentrated ammonium hydroxide with or without anhydrous ammonia addition, is described. The process preferably uses steam to strip ammonia from the biomass for recycling. The process yields of monosaccharides from the structural carbohydrates are good, particularly as measured by the enzymatic hydrolysis of the structural carbohydrates. The monosaccharides are used as animal feeds and energy sources for ethanol production.

Abstract: A method is provided for producing an L-amino acid by culturing a microorganism belonging to the Enterobacteriaceae family and having the ability to produce an L-amino acid, in a medium to produce and accumulate the L-amino acid in the medium. The microorganism has been modified by introduction of a DNA fragment which includes a pho regulon promoter and a structural gene encoding an L-amino acid biosynthetic enzyme, which is ligated downstream of the promoter so that the gene is expressed by the promoter, and so that the activity of the L-amino acid biosynthetic enzyme is increased by the expression of the gene by the promoter. In this way, the L-amino acid that is produced in the medium can be collected. Furthermore, the phosphorus concentration in the medium is such that the expression of the gene by the promoter is induced.

Abstract: A PHA copolymer comprising (R)-3-hydroxy-4-methyl valeric acid units and a production method thereof are provided. A polyhydroxyalkanoic acid copolymer comprising at least (R)-3-hydroxy-4-methyl valeric acid units; and a method of producing a polyhydroxyalkanoic acid copolymer comprising at least (R)-3-hydroxy-4-methyl valeric acid units, wherein in the presence of a carbon source and a precursor of (R)-3-hydroxy-4-methyl valeric acid, a transformant in which the gene of polyhydroxyalkanoic acid-polymerizing enzyme has been introduced in a microorganism selected from Escherichia coli, Ralstoniau sp., and Pseudomonas sp. is cultured, and from the culture obtained a polyhydroxyalkanoic acid copolymer comprising at least (R)-3-hydroxy-4-methyl valeric acid units is collected.

Abstract: This disclosure describes genetically modified photosynthetic microorganisms, including Cyanobacteria, that contain one or more exogenous genes encoding a diacylglycerol acyltransferase, a phosphatidate phosphatase, and/or an acetyl-CoA carboxylase, and which are capable of producing increased amounts of fatty acids and/or synthesizing triglycerides.

Abstract: The invention provides a glucose dehydrogenase that is an extremely stable enzyme having a thermostability of 80° C. or more, and that does not substantially act upon saccharides other than glucose (e.g., having a reactivity of less than 3% with respect to maltose, galactose, and xylose). The invention also provides a method for producing such an enzyme, and a composition for quantifying glucose using such an enzyme.

Abstract: An acetyl xylan esterase variant having perhydrolytic activity is provided for producing peroxycarboxylic acids from carboxylic acid esters and a source of peroxygen. More specifically, a Thermotoga maritima acetyl xylan esterase gene was modified using error-prone PCR and site-directed mutagenesis to create an enzyme catalyst characterized by an increase in specific activity. The variant acetyl xylan esterase may be used to produce peroxycarboxylic acids suitable for use in a variety of applications such as cleaning, disinfecting, sanitizing, bleaching, wood pulp processing, and paper pulp processing applications.

Abstract: An acetyl xylan esterase variant having perhydrolytic activity is provided for producing peroxycarboxylic acids from carboxylic acid esters and a source of peroxygen. More specifically, a Thermotoga maritima acetyl xylan esterase gene was modified using error-prone PCR and site-directed mutagenesis to create an enzyme catalyst characterized by an increase in specific activity. The variant acetyl xylan esterase may be used to produce peroxycarboxylic acids suitable for use in a variety of applications such as cleaning, disinfecting, sanitizing, bleaching, wood pulp processing, and paper pulp processing applications.

Abstract: A substrate or coating is provided that includes a lipase with enzymatic activity toward a component of a fingerprint. Also provided is a process for facilitating the removal of fingerprints is provided wherein an inventive substrate or coating including a lipase is capable of enzymatically degrading of one or more components of the fingerprint to facilitate fingerprint removal from the substrate or said coating. Applying heat to the substrate or coating increases the rate of fingerprint removal.

Abstract: A novel beta-glucosidase and nucleic acids encoding the beta-glucosidase. Also disclosed are cells, compositions, and methods relating to using the beta-glucosidase to convert ligocellulosic material to fermentable sugars.

Abstract: The present invention discloses a two-component genome flavivirus and a method for propagating such virus. Since the genetic material of this flavivirus is distributed between two genomes, the flavivirus is deficient in replication, incapable of causing disease but capable of inducing an immune response. Nevertheless, the design of the replication deficient flavivirus discussed herein allows propagation of these flaviviruses at industrial level.

Abstract: This disclosure describes genetically modified photosynthetic microorganisms, including Cyanobacteria, that contain one or more exogenous genes encoding a diacylglycerol acyltransferase, a phosphatidate phosphatase, and/or an acetyl-CoA carboxylase, and which are capable of producing increased amounts of fatty acids and/or synthesizing triglycerides.

Abstract: Novel strains of yeast and methods for improved ethanol production utilizing the yeast strains are disclosed. In particular, the novel yeast strains Saccharomyces cerevisae YE1358 and YE1615 provide for increased fermentation temperature tolerance, as well as tolerance to increased levels of glucose and ethanol, and thereby provide increased ethanol production as compared to ethanol industry standard strains of Saccharomyces cerevisae. The novel yeast strains also generate decreased residual glucose than the ethanol industry standard yeasts.

Abstract: The present invention relates to Trichoderma atroviride strains and their use as biological control agents or plant growth promoters. Methods and compositions for biological control of soil borne plant pathogens, and increasing plant yield using T. atroviride are also provided.

Abstract: The present invention provides for a process for preserving biological material. The process comprises subjecting the biological material to a fixation process and then packaging the biological material in a container under a controlled atmosphere of noble gas. In the process, the controlled atmosphere of noble gas utilized comprises one or more noble gases selected from argon, xenon, helium, neon, krypton and radon. The process optionally also utilizes one or more additional gases selected from nitric oxide, hydrogen, hydrogen sulfide, carbon monoxide, carbon dioxide, nitrogen and oxygen. This process allows for the long term storage of the biological material.

Abstract: This invention generally relates to an integrated ‘lab-on-a-Pipette’™ which will provide sample-to-answer single cell genetic diagnosis for preimplantation genetic diagnosis (PGD) and other forms of single cell analysis (SCA). SCA is a quickly growing field with substantial impact in prenatal testing, cancer biopsies, diabetes, stem cell research, and our overall understanding of heterogeneity in biology. However, single cell genetic analysis is challenging, inaccurate, and in many cases impossible, due to the small amount of sample (5 pg), and difficulties in handling small sample volumes (50-100 pL). The ‘lab-on-a-pipette’ device integrates a microaspiration tip with microfluidic analysis components to conduct in-situ, real-time single cell genetic diagnosis in a single device. The microaspiration tip extracts and encapsulate a cell into an ultra-low volume plug (˜300 pL).

Abstract: The present invention includes but is not limited to a specimen collection device that includes a chamber capable of collecting a specimen, a specimen passage slot, a reservoir, a reservoir seal, and a test device. A sample or specimen added to the chamber flows through the specimen passage slot into the reservoir. Flow into the reservoir may be limited by the reservoir seal. The test device positioned within the reservoir detects the presence or concentration of an analyte within the sample or specimen.

Abstract: A home test kit for detecting fecal blood includes a scoop device for collecting a fecal sample, a luminescent for mixing with the sample, a hollow container for containing the sample, water and the luminescent, or luminol during use of the kit. A base may be provided for supporting the container during testing, and the container may include an integrally formed lid. Detection of the blood in the sample is possible because the luminescent undergoes a light-producing reaction that involves, as a reactant or catalyst, blood or blood components or products. The blood is thus visible, or glows in darkened surroundings. The kit is compact, easy to use, and formed from biodegradable material for easy disposal.

Abstract: The present invention relates to a Drosophila in vitro system which was used to demonstrate that dsRNA is processed to RNA segments 21-23 nucleotides (nt) in length. Furthermore, when these 21-23 nt fragments are purified and added back to Drosophila extracts, they mediate RNA interference in the absence of long dsRNA. Thus, these 21-23 nt fragments are the sequence-specific mediators of RNA degradation. A molecular signal, which may be their specific length, must be present in these 21-23 nt fragments to recruit cellular factors involved in RNAi. This present invention encompasses these 21-23 nt fragments and their use for specifically inactivating gene function. The use of these fragments (or chemically synthesized oligonucleotides of the same or similar nature) enables the targeting of specific mRNAs for degradation in mammalian cells, where the use of long dsRNAs to elicit RNAi is usually not practical, presumably because of the deleterious effects of the interferon response.

Abstract: An agent containing a vinca alkaloid or its pharmacologically acceptable salt as an active ingredient can induce insulin production and/or secretion of non-neoplastic cells derived from the pancreas.

Abstract: Disclosed are novel stem cells of non-embryonic origins and the uses thereof.

Abstract: The present invention provides a fluid exchange cell culture technique and tissue repair cells (TRCs) made by these methods, as well as methods using these cells. The method includes a new wash step which increases the tissue repair properties of the TRCs of the invention. This wash step allows for the production of TRC populations with greater tissue repair and anti-inflammatory capabilities. Embodiments of the present invention include a post-culture process for cultured cells that preferably includes the steps of: a wash process for removing unwanted residual culture components, a volume reduction process, and a harvesting process to remove cultured cells. Preferably, all these steps are performed within a aseptically closed cell culture chamber by implementing a separation method that minimizes mechanical disruption of the cells and is simple to automate. The harvested cells may then be concentrated to a final volume for the intended use.

Abstract: The present invention relates to methods of generating an ex vivo tissue-like system in a bioreactor system capable of supporting continuous production of, and output of cells and tissues and an ex vivo tissue system made therefrom.

Abstract: Methods and devices for dispersion of clusters of somatic plant embryos suspended in a liquid are disclosed. The methods comprise i) subjecting the clusters of embryos to fluid dynamics forces causing axially extensional strain and radially compressional strain and ii) subjecting the clusters of embryos to fluid dynamics forces causing axially compressional strain and radially extensional strain fluid dynamics and iii) repeating said steps in sequence until the individual embryos are separated from each other. The devices may comprise a flow channel including at least one constriction, such that clusters of embryos flowing through the flow channel are first subjected to axially extensional strain and radially compressional strain, and then to axially compressional strain and radially extensional strain from fluid dynamics forces.