Abstract: The invention provides a gene encoding a protein selected from among the following proteins (a) to (c): (a) a protein having any of the amino acid sequences of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, and 108; (b) a protein which has an amino acid sequence equivalent to any of the amino acid sequences of (a), except that one to several amino acid residues are deleted, substituted, or added, and which exhibits cytokine production regulatory activity; and (c) a protein which has an amino acid sequence having 90% or higher identity to any of the amino acid sequences of (a), and which exhibits cytokine production regulatory activity, as well as a gene useful for regulating cytokine production and use of the gene.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed including those directed to STK12.

Abstract: Rotating a cartridge body 54 allows distribution ports and a combined distribution port provided in the cartridge body 54 and a channel inlet 53c provided in an upper surface of a ring array 53 to sequentially face a fluid port 30a of a reaction tank 30 independent of the cartridge body 54. Additionally, rotating the cartridge body 54 allows a plurality of DNA probes 53a to sequentially face a collimating lens 62a serving as a light detector independent of the cartridge body 54.

Abstract: Disclosed are a data processing and analysis method of gene expression data for identifying endogenous reference genes and a composition for the quantitative analysis of gene expression, comprising a pair of primers and/or probes useful in the amplification of the identified endogenous reference genes. Introduced with the concepts of “Zero's proportion’ and CV, the me allows different datasets to be integrally analyzed, thereby searching for novel reference genes. By the method, 2,087 genes are first found as housekeeping genes which are expressed in most tissues, and the usefulness thereof in the relative quantification of different target genes is determined by analyzing their expression stability. Out of the 2,087 genes, 13 genes are found to show higher expression stability with lower expression levels across a wide range of samples than traditional reference genes such as GAPDH and ACTB, and therefore are suitable for the normalization of universal genes having relatively low expression levels.

Abstract: A genetic marker including a SNP which can be used for assessing the risk of developing hypertension, a polynucleotide for assessing the risk of developing hypertension which can be used as a primer or probe for detecting the genetic marker, a method for assessing the risk of developing hypertension using the SNP, a microarray for assessing the risk of developing hypertension which is used for genotyping of the SNP, a kit used in the method for assessing the risk of developing hypertension, and the like.

Abstract: The present invention relates to the identification and use of gene expression profiles with clinical relevance to prostate cancer. In particular, the invention provides the identity of genes whose expression, at the transcriptional and protein levels, is correlated with prostate cancer progression. Methods and kits are described for using these gene expression profiles in the study and/or diagnosis of prostate cancer diseases, in the prediction of prostate cancer progression, and in the selection and/or monitoring of treatment regimens. The invention also relates to the screening of drugs that target these genes or their protein products, in particular for the development of therapeutics for modulating prostate cancer progression.

Abstract: A DNA chip and a prediction method for predicting the occurrence of a late adverse reaction in a urinary organ after C-ion RT are provided. The DNA chip comprises a supporting means for supporting a DNA probe thereon, and a plurality of genetic markers supported on the supporting means.

Abstract: The present invention provides an isolated HIV-1 mutant and isolated nucleic acid molecules comprising HIV-RT coding sequences harboring a novel mutation in the S68 codon, and in particular, deletions of the S68 codon. This novel deletion reduces the sensitivity of HIV to various nucleoside reverse transcriptase inhibitors. Methods of using this mutation for selecting effective antiretroviral agents in vitro and in vivo, methods for monitoring infection progression in HIV-infected individuals and methods for avoiding the emergence of and/or to treat individuals infected with HIV comprising mutations at the S68 codon of HIV-RT, e.g., S68del, are provided.

Abstract: Methods and compositions for selecting ES cells that are germline competent are provided, including gene expression arrays of from one to about 300 or more genes. Selecting ES cells that are competent for germline transmission by comparing the expression of one or more genes between an ES cell that is competent at germline transmission with an ES cell of interest is described. Selecting ES cells likely to be competent at germline transmission, based on their level of expression of gtl2, is also described.

Abstract: The invention relates to a method of indirectly identifying a polynucleotide comprising an open reading frame having an improved expression level from a library of polynucleotides encoding the same polypeptide of interest, or variants or homologues thereof, in a host cell expression library, the method comprising the steps of: a) providing an expression library in a host cell, said library comprising at least two different open reading frames encoding the same polypeptide of interest, or variants or homologues thereof, each open reading frame being translationally coupled to a downstream gene encoding a screenable or selectable reporter; b) culturing the host cell under conditions conducive to the expression of the polypeptide of interest, or variant or homologue thereof; and c) screening and/or selecting for a host cell having an improved expression level of the translationally coupled reporter when compared to one or more other host cells of the library, thus indirectly identifying a polynucleotide comprisi

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

Abstract: The invention provides compositions and methods for determining the likelihood of successful treatment with anti-angiogenic antibodies or equivalent thereof, in combination with a pyrimidine based antimetabolite and a platinum-based alkylating agent based therapy. The methods comprise determining the genomic polymorphism present in a predetermined region of a gene of interest and correlating the polymorphism to the predictive response. Patients identified as responsive are then treated with the appropriate therapy.

Abstract: The present invention concerns double stranded RNA compositions and transgenic plants capable of inhibiting expression of genes essential to establishing or maintaining nematode infestation in a plant, and methods associated therewith. Specifically, the invention relates to the use of RNA interference to inhibit expression of a target plant gene, which is an MTHFR-like gene, and relates to the generation of plants that have increased resistance to parasitic nematodes.

Abstract: The present invention features improved in vitro RNA display libraries to allow reliable expression and selection of scFv antibody molecules from expression libraries. The scFv antibody libraries of the invention contain an optimized, shortened inter-domain linker that improves expression scFv antibody expression. The scFv antibody libraries also include short nucleic acid barcodes that allow for identification of individual library clones, libraries or subsets thereof. Primers for generating, amplifying and spectratyping the scFv antibody libraries of the invention are also provided.

Abstract: Provided herein are methods for generating diverse polypeptide and nucleic acid molecule libraries and collections, and the collections and libraries; methods for selecting variant polypeptides and nucleic acid molecules from the libraries; and molecules selected from the libraries. Exemplary of the polypeptides and nucleic acid molecules are antibodies and nucleic acids encoding the antibodies (including antibody fragments and domain exchanged antibodies). Also provided herein are methods of displaying polypeptides such as antibodies, for example on the surface of genetic packages, such as phage; and libraries and collections of the displayed polypeptides and vectors for producing the displayed polypeptides, libraries and collections. Exemplary of the displayed antibodies are domain exchanged antibodies.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rationale design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes.

Abstract: The present invention relates to a method for prognosing or classifying cancer subtypes in a subject with breast cancer. Methods and biomarkers are disclosed that are useful for prognosing or classifying ESR1, PGR and ERBB2 breast cancer subtypes.

Abstract: An impedance spectroscopy system and method are provided for quantitatively measuring DNA. The method provides a transducer having electrode surfaces exposed to a shared local environment. The electrode surfaces are functionalized with an oligonucleotide to interact with a predetermined DNA target. A DNA sample solution is introduced into the local environment. The solution includes nucleotides, polymerase enzyme, and primers. The DNA sample is thermocycled to promote a first DNA target polymerase chain reaction (PCR). Then, capacitance is measured between a pair of transducer electrodes, and in response to measuring the capacitance, a determination is made of the presence of first DNA amplicons in the DNA sample. Typically, a number of thermocycles are performed and capacitance measurements are made after each cycle, so that an amplicon growth rate can be determined.

Abstract: This invention relates to a prophylactic and/or therapeutic treatment of footrot, and in particular to a vaccine effective in prophylactic and/or therapeutic treatment of footrot. Specific polypeptides of Dichelobacter nodosus have been identified as vaccine candidates. In some embodiments the polypeptide is expressed more strongly when the bacterium is grown in vivo or is expressed more strongly in the presence of ovine hoof powder. In other embodiments the polypeptide are reactive against sera recovered from animals repeatedly infected with D. nodosus.

Abstract: The invention relates to a procedure for linking cognate pairs of VH and VL encoding sequences from a population of avian cells enriched in particular surface antigen markers. The linking procedure involves a multiplex molecular amplification procedure capable of linking nucleotide sequences of interest in connection with the amplification (multiplex PCR). The method is particularly advantageous for the generation of cognate pair libraries as well as combinatorial libraries of antibody variable region encoding sequences from chickens or other birds. The invention also provides methods for generation of chimeric human/avian antibodies and expression libraries generated by such methods.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed including those directed to COPB2.

Abstract: The present invention discloses a bio-reaction module, the so called mini bio-reactor, for providing a stable environment for the hybridization or immuno-reaction on biochips with constant temperature and humidity. Moreover, the mini bio-reactor can be a tool for studying the bio-reaction mechanism. Any variations in bio-reaction mechanism and environmental factors may affect experiment outcomes. Hence, when bulky equipment is miniaturized into a module system, the researchers can utilize a mini bio-reactor to perform bio-experiments or reactors in series connection to perform batch experiments. The structure design of mini reactor is able to promote better reaction efficiency and to shorten reaction time for a variety of bio experiments. Hence what is developed is an automatic, handy and inexpensive device for bio researches with high sensitivity and reliability.

Abstract: The present invention relates to a vector library comprising a multiplicity of different eukaryotic secretion vectors, wherein each vector comprises under the control of transcriptional and translational control sequences a gene encoding for an extracellular soluble fusion polypeptide which gene comprises a coding sequence for a scaffold polypeptide linked to variable coding sequences for a peptide, wherein said vectors comprise a nucleic acid coding for a secretory signal sequence linked to the gene coding for the fusion polypeptide.

Abstract: Systems and methods employing combinatorial arrays for revealing factors which control biomineralization processes. An understanding of such control factors may be expected to allow those of skill in the art to mimic biomineralization processes so as to allow manufacture of engineered synthetic biomineralized products, such as artificial bones. Such products would be expected to have structure and properties similar or identical to natural products (e.g., bones), and exhibit improved immunological acceptance when implanted as compared to existing synthetic engineered products.

Abstract: Disclosed are substrates for detecting one or more target molecules and methods for detecting molecules using surface plasmon resonance.

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity. The libraries are designed to reflect the preimmune repertoire naturally created by the human immune system, with or without DH segments derived from other species, and are based on rational design informed by examination of publicly available databases of antibody sequences.

Abstract: Provided herein are modified OB-fold domains having desired properties; methods of producing libraries of modified OB-fold domains; the libraries of modified OB-fold domains produced by such methods; methods for screening such libraries of modified OB-fold domains for desired biological activities; and the modified OB-fold domains identified from such libraries. Provided herein are modified OB-fold domains obtainable from Pyrobaculum aerophilum that exhibit modified binding interactions.

Abstract: The present application describes a base-modified RNA and the use thereof for increasing the expression of a protein and for the preparation of a pharmaceutical composition, especially a vaccine, for the treatment of tumours and cancer diseases, heart and circulatory diseases, infectious diseases, autoimmune diseases or monogenetic diseases, for example in gene therapy. The present invention further describes an in vitro transcription method, in vitro methods for increasing the expression of a protein using the base-modified RNA, and an in vivo method.

Abstract: The present invention concerns a method of producing a desired gene product in a recombinant gene expression system, said method comprising expressing said gene from a Pm promoter-based expression system using at least two mutant elements selected from: (i) a mutant Pm promoter; (ii) a mutant mRNA leader; and (iii) a mutant XyIS; wherein said mutant elements each comprise one or more mutations which enhance expression of said desired gene. Particularly combinations of a mutant Pm promoter and a mutant mRNA leader are concerned. Isolated nucleic acid molecules, vectors, host cells, libraries, expression systems, methods of enhancing expression, obtaining nucleic acid molecules and identifying combination mutants which enhance expression, artificially constructed operons and their uses are also encompassed.

Abstract: The invention provides a method for identification of alleles. In this method, genomic DNA is used as target. Multiple allele-specific PCR amplification are carried out with a group of primers comprising one or more allele-specific primers for a target gene, a universal primer, and a common primer; and a DNA polymerase without 5? to 3? exonuclease activity. The PCR products are hybridized with tag probes immobilized on a DNA chip. Results are determined based on the signal intensity and the position of the probe immobilized on the array. Each allele-specific primer comprises a unique tag sequence at the 5? end. Each tag probe immobilized on the DNA chip comprises a sequence identical to its corresponding tag sequence; and each tag probe hybridizes only with the complementary sequence in the PCR amplification product.

Abstract: Identified herein are different forms of bitter receptor genes that occur in different humans. These alleles are generated by numerous coding single nucleotide polymorphisms (cSNP's) that occur within the members of the T2R gene family. Some SNP's cause amino acid substitutions, while others introduce chain termination codons, rendering the allele non-functional. Differences in these genes are believed to have a large effect on those individuals' sense of bitter taste, such that these individuals perceive the taste of bitter substances differently than the rest of the population. The ability to assay this allelic information is useful in the development of flavorings and flavor enhancers, as it can be used to define large groups and populations who perceive bitter tastes differently. This in turn allows the taste preferences of these groups to be addressed at the molecular level for the first time.

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

Abstract: Provided herein are pregnancy specific marker genes, such as those shown in Tables I-III, and methods of detecting the same to determine bovine pregnancy.

Abstract: The invention provides a method for characterising a sample comprising nucleic acid derived from a cell. The method comprises determining whether a sample comprises at least a minimal sequence of at least one new microRNA (miRNA) according to the invention or a mammalian ortholog thereof and characterizing the sample on the basis of the presence or absence of the miRNA. The invention further provides nucleic acid molecules and collections thereof and their use in therapeutic and diagnostic applications. The invention furthermore provides a method for identifying a miRNA molecule or a precursor molecule thereof.

Abstract: It is an object of the present invention to provide a method for producing a biomolecule assay chip using a microreactor technique, and a chip produced by the method.

Abstract: The present invention relates to a method and kit, including parts thereof, for the prognosis of breast cancer. In particular, the method involves identifying a gene expression pattern, or molecular signature, that indicates the likelihood of survival of a patient with breast cancer, and/or likelihood of recurrence of the disease in a patient being treated, or having been treated, for breast cancer, and the likelihood of a patient having a metastatic form of cancer. Six molecular signatures, comprising twelve groups/sets of molecular markers have been identified, which have relevance in determining the prognosis of a given breast cancer. Each molecular signature comprises a plurality of genetic markers whose expression, either high or low in respect of normal tissue, is indicative of a given outcome, such as survival or recurrence.

Abstract: The present invention provides improved methods and compositions for RNA isolation. In particular embodiments the present invention concerns the use of methods and compositions for the isolation of full-length RNA from fixed tissue samples. The present invention provides methods for digesting and extracting RNA from a fixed tissue sample.

Abstract: Disclosed are a nucleic acid chip for obtaining binding profiles between unknown biomolecules and single-stranded nucleic acids, a method for manufacturing the chip, and a method for analyzing the unknown biomolecules using the chip. The nucleic acid chip is used to analyze biological significance of the unknown biomolecule in the biospecimen. The nucleic acid chip can be manufactured by reacting a biospecimen containing an unknown biomolecule with random single-stranded nucleic acids having random base sequences to determine biomolecule-binding single stranded nucleic acids capable of binding the unknown biomolecule; and synthesizing capture single stranded nucleic acids composed of the determined biomolecule-binding single stranded nucleic acids and/or single stranded nucleic acids having base sequences complementary to those of said determined biomolecule-binding single stranded nucleic acids and affixing the capture single stranded nucleic acids on a substrate.

Abstract: Provided is a set of mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, each mass label in the set having a common mass; wherein the set comprises a plurality of groups of mass labels, the mass of the mass marker moiety being the same for mass labels within a group, the mass of the mass marker moiety being different between groups; the mass marker moiety is capable of fragmentation into two or three fragments; and the mass of at least one fragment of the mass marker moiety differs between mass labels within a group.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rationale design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Through these methodologies, one can select siRNA that target genes, including surviving.

Abstract: As noted above, certain aspects of this disclosure relate to a library of nucleic acid vectors, as well as a method for making the same. In certain embodiments, the library of nucleic acid vectors comprises: a plurality of nucleic acid molecules of the following formula: S1—R—S2 wherein, in each nucleic acid of the plurality: S1 and S2 are each at least 15 nucleotides in length; S1 and S2 are complementary to each other along their entire length; either S1 or S2 is complementary along its entire length to a sequence in eukaryotic mRNA; and R is a six base recognition site for a restriction endonuclease; and wherein S1 and S2 vary in nucleotide sequence between different members of the plurality. A method for amplifying a circular nucleic acid is also provided.

Abstract: Simple and convenient methods for arranging molecules of interest in a pre-determined pattern are described. The methods use combinatorial hybridization based on interactions between complementary nucleic acid sequences to arrange the molecules of interest. The resulting arrangements, kits containing the components used in the methods, and methods of using the resulting arrangements are also disclosed.

Abstract: The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.

Abstract: Provided are methods for using nucleic acid sequences having two or more degenerately pairing nucleotides, each degenerate nucleotide having a partially overlapping set of complementarity, to reduce the number of hybridizing nucleotide sequences or probes used in biochemical and molecular biological operations having sequence specific hybridization. The method may be employed for various hybridization procedures with sequence specific hybridization, including sequencing methods measuring hybridization directly, and tagging by hybridization methods in which the sequence is determined by analyzing the pattern of tags that hybridize thereto, and hybridization dependent amplification methods.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed.

Abstract: The present invention is related to a method for preparing a nucleic acid library comprising a plurality of various elements or nucleic acid molecules that differ in a controlled manner at one or several distinct nucleotide positions.

Abstract: The invention generally provides compositions and methods of using a subject's genetic information for the selection of prophylactic or therapeutic agents and treatment regimens, and related methods for assaying the risk of an adverse cardiovascular event in the patient.

Abstract: [PROBLEMS] To provide: a gene marker or a protein marker for detecting whether or not an Aurora A inhibitor acts in a living body in an Aurora A-specific manner when the Aurora A inhibitor is administered to the living body; and a method for predicting or diagnosing the pharmacological efficacy of an Aurora A inhibitor by using the gene marker or the protein marker [MEANS FOR SOLVING PROBLEMS] A gene/protein marker for use in the prediction or diagnosis of the pharmacological efficacy of an Aurora A inhibitor, wherein the gene is a gene selected from the group consisting of Aurora B, Histone H3, BIRC5, PRC1, DLG7, TACC3 and KNTC2 or a gene having substantially the same function as that of the gene; and a method for predicting or diagnosing the pharmacological efficacy of an Aurora A inhibitor by using the gene/protein marker.

Abstract: Control beads are disclosed that allow for improved quantitation of analytes in multiplexed bead assays. The control beads have a range of concentrations of calibration moieties that provide for the preparation of a titration curve. The titration curve can be used to quantify the concentration of the analytes. The titration curve can be used to correlate the signal obtained from a bead with the concentration (or absolute number of molecules) of the analyte bound to the bead.

Abstract: The present invention concerns double stranded RNA compositions and transgenic plants capable of inhibiting expression of genes essential to establishing or maintaining nematode infestation in a plant, and methods associated therewith. Specifically, the invention relates to the use of RNA interference to inhibit expression of a target CAD-like plant gene, and relates to the generation of plants that have increased resistance to parasitic nematodes.