Abstract: The invention relates to a method for the in vitro detection and/or differentiation and/or progress observation of pathophysiological conditions with the aid of sample nucleic acids, including determination of gene activities by means of a plurality of polynucleotides, determination of gene activities of at least one internal reference gene, and formation of an index value from the single determined normalized gene activities of a multigene biomarker indicating the pathophysiological condition.

Abstract: The invention relates to diagnostic methods to predict whether a subject is predisposed for acquiring a disease or to predict the therapy responsiveness of an individual patient. Provided is a method for determining whether a subject is predisposed for developing an autoimmune disease, comprising determining in a sample isolated from said subject the amount of intact genes, or gene products thereof, of the Fc?RII/Fc?RIII gene cluster, said gene cluster comprising the FCGR2C, FCGR3A, FCGR2A and FCGR3B genes encoding an activating Fc?R, and FCGR2B encoding an inhibitory Fc?R; and correlating said amount to the amount observed in a healthy population. Also provided is a method to predict the responsiveness of a subject to therapy with intravenous immunoglobulin (IVIg) therapy or a monospecific biological, such as a humanized or human monoclonal antibody or a chimeric molecule, comprising the C-terminal Fc-tail of IgG.

Abstract: A method of detecting a target substance includes providing a number of molecular tethers at a channel surface of a sensor such that at least some of a plurality of beads, as a result of a biological interaction between a target substance and the tethers, are attached to the channel surface by the tethers or released from the channel's surface by cleaving the tethers. This method further includes introducing an analyte into the channel and determining the population of beads at the channel surface to indicate a presence of the target substance in the analyte.

Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.

Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.

Abstract: The present invention relates to agents, and methods for identifying compounds, which agents and compounds result in the modulation of cellular trafficking of proteins in particular that of CF-associated mutant Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). In addition, the invention relates to compositions and methods for the use thereof in treating conditions that are characterized by an ER-associated protein misfolding and abnormal cellular trafficking of disease-associated proteins, including cystic fibrosis (CF).

Abstract: The invention pertains to a method of determining a statin dosage for an individual in need of treatment with a statin, comprising determining a SLCO1B1 genotype from a nucleic acid sample of the individual, said genotype comprising the presence or absence of the SLCO1B1-056 polymorphism, and determining an ApoE genotype or phenotype identifying an ApoE polymorphism selected from the group consisting of ApoE2, ApoE3, ApoE4, and any combination thereof, wherein the combination of a SLCO1B1 genotype identifying the presence of the SLCO1B1-056 C polymorphism and the ApoE genotype or phenotype identifying one of the ApoE3/4 or ApoE4/4 genotypes indicates the statin dosage.

Abstract: A method and assay kit for determination of thymidine kinase (TK) activity in a biological sample, such as blood, serum, plasma, Cerebral Spinal Fluid (CSF), pleural fluid, ascites, tissues, cells and extracts thereof, is described. The method comprises contacting, in a buffer, a Basic Reaction Mixture comprising: solid surface-attached primer and/or template, a modified deoxy nucleoside, such as BromodeoxyUridine, IododeoxyUridine, Fluorodeoxy-Uridine or VinyldexoyThymidine as a kinase enzyme substrate, a phosphate donor, a nucleotide polymerizing enzyme, and a kinase enzyme source devoid of TK activity, such as a yeast extract, with the biological sample. After incubation the amount of modified deoxy nucleoside that has been incorporated into the solid surface-attached primer and/or template, is determined and the TK activity present in the biological sample is directly proportional to the amount of incorporated modified deoxy nucleoside.

Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.

Abstract: Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.

Abstract: The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template.

Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.

Abstract: The present disclosure provides methods for assessing a patient's cancer risk and/or recurrence risk, which methods comprise assaying, in a biological sample obtained from the gastrointestinal (GI) tract of the patient, an expression level of a risk gene. The present disclosure also provides methods involving a cancer risk/recurrence risk sequence, i.e. the V600E mutation of the BRAF gene, which is useful for assessing cancer risk and/or recurrence risk in a patient.

Abstract: A novel ligand conjugate which is effectively utilizable for analyzing a function of a protein; a ligand-supporting object; and a method of analyzing a protein. The ligand conjugate has a structure which comprises: a linker compound having a structure represented by the following General Formula (1): (wherein n and p each is an integer of 0 to 6) in which X is a structure comprising one, two, or three hydrocarbon derivative chains which have an aromatic amino group at the end and may have a carbon-nitrogen bond in the main chain, Y is a hydro-carbon structure containing one or more sulfur atoms, and Z is a straight-chain structure comprising a carbon-carbon bond or carbon-oxygen bond; and a sugar which has a reducing end and is bonded to the linker compound through the aromatic amino group.

Abstract: The disclosure provides, among other aspects, neutralizing antibodies and portions thereof that bind to ActRIIB and uses for same.

Abstract: A method and device to detect Hepatitis C (HCV) antibodies in oral fluid is provided. This method introduces a non-antibody detection molecule that labels all classes of patient antibodies in oral fluid, followed by the specific concentration of labeled anti-HCV antibodies by selective capture in a trapping zone consisting of peptide antigens derived from the HCV genome. Signal generated by the labeled antibodies present in the trapping zone is proportional to the number of anti-HCV antibodies bound to the antigens present in the trapping zone. Presence of signal derived from the capture of antibody/detection molecule complexes in the trapping zone is indicative of past exposure to HCV.

Abstract: Provided are methods and compositions for determining whether an individual has Sjögren's disease (SD). The method entails determining in a biological sample from the individual the presence of antibodies directed to salivary gland protein 1 (SP-I), parotid secretory protein (PSP), carbonic anhydrase 6 (C A6), or determining a combination of the antibodies. Determining that the individual has SD is based on the presence of the antibodies. The method provides for detection of early SD. Kits for antibody detection containing the antigens to which the antibodies of SD patients are directed are also provided.

Abstract: We provide VHZ for use in a method of treatment, prophylaxis or alleviation of a cancer, such as breast cancer, in an individual. We provide an anti-VHZ agent for the treatment, prophylaxis or alleviation of cancer. We further provide a kit for detecting breast cancer in an individual or susceptibility of the individual to breast cancer comprising means for detection of VHZ expression in the individual or a sample taken from him or her as well as a method of detecting a cancer cell, the method comprising detecting modulation of expression, amount or activity of VHZ in the cell.

Abstract: The invention relates to the identification of genetic products expressed in association with tumors and to coding nucleic acids for said products. The invention also relates to the therapy and diagnosis of diseases in which the genetic products are aberrantly expressed in association with tumors, proteins, polypeptides and peptides which are expressed in association with tumors and to the coding nucleic acids for said proteins, polypeptides and peptides.

Abstract: Squamous carcinoma stem cells (SCSC) are identified. The cells can be prospectively isolated or identified from primary tumor samples, and are shown to possess the unique properties of cancer stem cells in functional assays for cancer stem cell self-renewal and differentiation, and to form unique histological microdomains useful in cancer diagnosis.

Abstract: A method and kit for assaying a cell sample for the presence of at least a threshold number of cells of a given type are disclosed. The kit includes an assay device having a sample chamber for receiving the cell sample and an elongate collection chamber containing a selected-density and/or viscosity medium and having along its length, a plurality of cell-collection regions, and particles which are capable of specific attachment to cells of the selected cell type, and which are effective, when attached to the cells, to increase the density or magnetic susceptibility of the cells. In operation, particle-bound cells and particles in the cell sample are drawn through the elongate collection chamber under the influence of a gravitational or selected centrifugal or magnetic-field force until the particle-bound cells and particles completely fill successive cell-collection regions in the collection chamber.

Abstract: The present invention relates to methods and kits for diagnosing, ascertaining the clinical course of myelodysplastic syndrome (MDS) and ascertaining response to a therapy regimen of myelodysplastic syndrome. Specifically the invention provides methods and kits useful in the diagnosis and determination of clinical parameters associated with MDS based on surface markers unique to MDS.

Abstract: An affinity ligand-matrix conjugate of the structure Z-Spacer-[NX-A]m-NY-A-NK2 is useful for the isolation, separation, purification, characterization, identification or quantification of endotoxins in an aqueous system, wherein m is an integer of at least one; each A independently represents an optionally substituted linear, branched or cyclic saturated hydrocarbon chain containing 1 to 6 carbon atoms; each X independently represents hydrogen or alkyl; Y is X or A-NX2; and Z is a support matrix attached to the ligand through an optional spacer arm (Spacer).

Abstract: A method for specifically quantifying HDL cholesterol in which cholesterol in lipoproteins other than HDL is erased in the first step, and HDL cholesterol is specifically quantified in the second step, by which accurate values can be obtained even in measurements of abnormal samples such as disorder of lipid metabolism and lipoprotein abnormality, is disclosed.

Abstract: A presence/absence test for Staphylococcus aureus (S. aureus) involves placing a first generation test sample in a solution that will clot in the presence of S. aureus. The solution contains components that will selectively grow S. aureus and also contains clotting factors that will react with S. aureus, if S. aureus is present in the sample, to clot the solution. Examples of specimen samples that can be tested include nasal swabs and lesion swabs, among others. The test can also be modified to detect the presence or absence of methicillin resistant S. Aureus (MRSA).

Abstract: Methods of screening a test agent for activity to modulate an oxidative demethylation enzyme are provided according to embodiments of the present invention which includes preparing a test reaction comprising an oxidative demethylation enzyme, a substrate for the oxidative demethylation enzyme, a test agent and 4-amino-3-penten-2-one under conditions which allow generation of formaldehyde by oxidative demethylation of the substrate by the enzyme in the absence of the test agent; detecting fluorescence in the test reaction, the fluorescence indicative of reaction of formaldehyde and 4-amino-3-penten-2-one in the test reaction; and comparing fluorescence detected in the test reaction with a control, wherein a difference in detected fluorescence is indicative of a change in activity of the oxidative demethylation enzyme in the presence of the test agent.

Abstract: A cell dispersion method, a cell dispersing agent and a cell measurement method, each of which can disperse a cell mass while reducing damage to a cell are provided. Upon dispersing a cell mass, a fluororesin particle is used. A cell mass composed of an aggregated of multiple cells is mixed with a fluororesin particle in a liquid medium, thereby separating the cell mass into individual cells to disperse the cells. In addition, the dispersed cells are measured by flow cytometry, thereby carrying out cell measurement.

Abstract: A biological indicator for determining the effectiveness of a sterilization process is disclosed having a package and carrier integral therewith. The package includes a first sheet and a second sheet having a bottom portion, side portions and a top portion. The first and second sheets are joined together generally along a periphery of the first and second sheets by a peelable adhesive. A carrier having a plurality of spores thereon for determining the effectiveness of a sterilization process is attached to the package between the first and second sheets and at least a portion of the resealable adhesive. The package may be opened and subsequently partially or fully closed to enclose the carrier.

Abstract: Disclosed are culture media, protocols and kits for diagnosis of toxigenic Clostridium difficile, where the culture medium comprises Cooked Meat Medium with glucose; yeast extract; taurocholate; cycloserine; and cefoxitin.

Abstract: The present invention relates to a method for the semi-quantitative determination of cariogenic bacteria in a sample of saliva and/or plaque, in which the microorganisms contained in a sample of plaque or saliva are brought into contact with a carbon source that is fermented to acid by the cariogenic bacteria. The microorganisms are then incubated under conditions which make possible selective acid formation by the cariogenic bacteria. The acid formation is then detected by determining the pH at least once within a period of 12 hours after adding the carbon source, wherein the cariogenic bacteria are determined semi-quantitatively in the sample by comparison of the pH with at least one reference value. In addition, the invention provides kits for carrying out such methods.

Abstract: A method and apparatus for producing histological sections by means of a microtome are suggested. A histological section of predefined thickness is produced with a microtome from a block comprising a tissue sample. A carrier material is applied with an application apparatus onto the block prior to before production of the histological section. To ensure that the histological sections do not roll up, and to enable improved downline processing of the histological sections as compared with a carrier material embodied in the form of an endless strip and that the carrier material is cut out prior to application to a size and/or a shape that corresponds substantially to the cross-sectional area of the block; and that the cut-out carrier material is then applied onto the block. The suggested apparatus is designed to apply the carrier material onto a histological section to be prepared by a microtome.

Abstract: The present invention relates to a copolymer comprising 3-hydroxyalkanoate monomer unit and lactate monomer unit, or their preparing method. More specifically, the present invention relates to a method for preparing a copolymer comprising lactate monomer and 3-hydroxyalkanoate monomer, wherein the method comprises culturing a cell or plant comprising the gene of enzyme converting lactate and 3-hydroxyalkanoate into lactyl-CoA and 3-hydroxyalkanoyl-CoA, respectively, and polyhydroxyalkanoate synthase gene together, and the copolymer made by the method. The copolymer of the present invention is a biodegradable polymer being able to be usefully used instead of conventional synthetic plastic, and the copolymer can be used also for medical use.

Abstract: The present invention provides methods of producing a product or product precursor of a biosynthetic pathway in a genetically modified host cell. The present invention also provides genetically modified host cells comprising nucleic acids encoding a scaffold polypeptide and nucleic acids comprising nucleotide sequences encoding two or more enzymes in a biosynthetic pathway. The present invention further provides nucleic acids comprising nucleotide sequences encoding scaffold polypeptides, for use in a subject method.

Abstract: Some aspects of this invention relate to methods useful for the conversion of a carbon source to a biofuel or biofuel precursor using engineered microbes. Some aspects of this invention relate to the discovery of a key regulator of lipid metabolism in microbes. Some aspects of this invention relate to engineered microbes for biofuel or biofuel precursor production.

Abstract: A sugar liquid containing only very small amounts of fermentation-inhibiting substances is produced by a method for producing a sugar liquid using a cellulose-containing biomass as a raw material, the method including: (1) a step of hydrolyzing a cellulose-containing biomass to produce an aqueous sugar solution; and (2) a step of filtering the obtained aqueous sugar solution through a nanofiltration membrane and/or reverse osmosis membrane to collect a purified sugar liquid from the feed side, while removing fermentation-inhibiting substances from the permeate side.

Abstract: The invention provides a chimeric E2 enzyme comprising a Ubc domain fused to a heterologous ubiquitin binding domain (UBD). The chimeric enzymes of the invention may be useful in producing elevated levels of free polyubiquitin.

Abstract: An L-amino acid is produced by culturing an L-amino acid-producing bacterium which belongs to the Enterobacteriaceae family and which has been modified so that the activity of an iron transporter is increased by enhancing expression of one or more genes of the following genes: tonB gene, fepA gene, and fecA.

Abstract: The present invention provides a bacterium having a genome that is genetically engineered to be smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.

Abstract: Compounds and methods are described for producing protein compositions having reduced amounts of O-linked glycosylation. The method includes producing the protein in cells cultured in the presence of certain benzylidene thiazolidinediones inhibitors of Pmt-mediated O-linked glycosylation.

Abstract: The present disclosure relates to host cells containing a recombinant polynucleotide encoding a polypeptide where the polypeptide transports cellodextrin into the cell. The present disclosure further relates to methods of increasing transport of cellodextrin into a cell, methods of increasing growth of a cell on a medium containing cellodextrin, methods of co-fermenting cellulose-derived and hemicellulose-derived sugars, and methods of making hydrocarbons or hydrocarbon derivatives by providing a host cell containing a recombinant polynucleotide encoding a polypeptide where the polypeptide transports cellodextrin into the cell.

Abstract: The subject invention provides an improved process for the production of human growth hormone.

Abstract: The invention relates to a method of preparing heteromultimeric polypeptides such as bispecific antibodies, bispecific immunoadhesins and antibody-immunoadhesin chimeras. The invention also relates to the heteromultimers prepared using the method. Generally, the method provides a multispecific antibody having a common light chain associated with each heteromeric polypeptide having an antibody binding domain. Additionally the method further involves introducing into the multispecific antibody a specific and complementary interaction at the interface of a first polypeptide and the interface of a second polypeptide, so as to promote heteromultimer formation and hinder homomultimer formation; and/or a free thiol-containing residue at the interface of a first polypeptide and a corresponding free thiol-containing residue in the interface of a second polypeptide, such that a non-naturally occurring disulfide bond is formed between the first and second polypeptide.

Abstract: This invention relates to a cell culture process for the production of polypeptides in mammalian CHO cells characterized by one or more temperature and pH shifts which are adjusted in respect to their timing and step size to reduce cell death, increase product yield and improve product quality.

Abstract: Certain embodiments provide a GPCR fusion protein. In particular embodiments, the GPCR fusion protein comprises: a) a G-protein coupled receptor (GPCR); and b) an autonomously folding stable domain, where the autonomously folding stable domain is N-terminal to the GPCR and is heterologous to the GPCR. The GPCR fusion protein is characterized in that is crystallizable under lipidic cubic phase crystallization conditions. In certain embodiments, the GPCR fusion protein may be crystallizable in a complex with a G-protein or in a complex with an antibody that binds to the IC3 loop of the GPCR.

Abstract: The present invention provides a method of increasing protein production in a cell culture by growing cells that produce the protein (e.g., the growth phase) in a perfusion cell culture to a high cell density (i.e., at least above about 40×106 cells/N mL) and then switching to a protein production phase, wherein the cells are cultured in a fed-batch cell culture. The present invention further provides a method for clarifying a protein from a cell culture by adjusting the pH of the cell culture to below neutral pH (i.e., below a pH of 7) and settling the cell culture, such that the cell culture separates to form a supernatant layer and a cell-bed layer, wherein the protein is in the supernatant layer.

Abstract: The present invention aims to provide a particulate composition containing anhydrous crystalline 2-O-?-D-glucosyl-L-ascorbic acid having a significantly, hardly solidifiable property compared to conventional ones in a grade for use in quasi-drugs; a process for producing the same; and uses thereof. The present invention solves the above object by providing a particulate composition containing anhydrous crystalline 2-O-?-D-glucosyl-L-ascorbic in an amount of over 98.0% by weight but less than 99.9% by weight, on a dry solid basis; or a degree of crystallinity of 90% or higher for anhydrous crystalline 2-O-?-D-glucosyl-L-ascorbic acid; and by providing a process for producing the same and uses thereof.

Abstract: Primers for DNA elongation are immobilized onto a substrate having on the surface thereof a polymer substance which contains a first unit having a group derived from a phosphoester composing the hydrophilic section of a phospholipid, and a second unit having an activated ester group, and DNA elongation reaction is allowed to proceed in a reaction system having introduced therein a sample which contains DNA fragments having desired sequences and nucleotide monomers, by heating the reaction system up to a temperature causing thermal unfolding of the DNA chains, and then by cooling the reaction system down to a temperature for annealing.

Abstract: The present invention provides compositions and methods for the detection and characterization of HPV sequences. More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay) to screen nucleic acid samples, e.g., from patients, for the presence of any one of a collection of HPV sequences. The present invention also provides compositions, methods and kits for screening sets of HPV sequences in a single reaction container.

Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.

Abstract: The present invention relates to a novel method for preparing pterocarpan from isoflavan-4-ol. With the use of the method of the present invention, the absolute configuration of C3 and C4 positions on the B-ring of isoflavan-4-ols is maintained identically also in pterocarpans, and thus, enantiopure pterocarpans can be efficiently prepared.