Abstract: Methods of determining the activity of an immunomodulatory compound by measuring the presence of an miRNA in a sample are disclosed. Additionally disclosed are methods of assessing the patient compliance in patients treated with an immunomodulatory compound.

Abstract: The present invention relates in general to human genetic polymorphisms and their association with human health and to methods and materials for analyzing allelic variations, and to the use of genetic polymorphisms in the diagnosis and treatment of smoking behavior and nicotine dependence. Provided herein are methods for determining risk in a subject of developing regular smoking behavior. Also provided are primers, probes, microarrays, and kits related thereto.

Abstract: This document relates to methods and materials involved in detecting tissue injury and/or rejection (e.g., injury and/or rejection of transplanted tissue). For example, this document relates to methods and materials involved in the early detection of kidney tissue injury.

Abstract: Disclosed are libraries of chimeric zinc finger domains. The libraries can include two or more zinc finger domains from naturally occurring proteins, e.g., mammalian proteins and particularly human proteins. Useful chimeric zinc finger domains can be identified from the library. Also disclosed are the amino acid sequences of zinc finger domains that recognize particular sites.

Abstract: The present invention relates to compositions suitable for spotting compounds onto a substrate, and methods employing these compositions. The composition can include one or more organic anions of formula I: R(X)m(Y)n. In an embodiment of formula I, R is an organic moiety, X is an anionic moiety, and, Y is a neutral hydrophilic moiety. The composition can include one or more neutral hydrophilic polymers. In an embodiment, the neutral hydrophilic polymer can be represented by formula V: In Formula V, the group in parenthesis represents the polymer backbone, A can be absent or is a carbon or a heteroatom, and B is pendant neutral hydrophilic group. The present invention includes arrays, which can be made with or include compositions according to the present invention and can be made by using the method of the present invention.

Abstract: The invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides and also the use of the 5? and 3? modified library of templates in methods of solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, wherein over-representation of “end” sequences of the primary polynucleotide molecules from whence the 5? and 3? modified library is generated is greatly reduced or prevented.

Abstract: The present invention concerns methods and compositions for introducing miRNA activity or function into cells using synthetic nucleic acid molecules. Moreover, the present invention concerns methods and compositions for identifying miRNAs with specific cellular functions that are relevant to therapeutic, diagnostic, and prognostic applications wherein synthetic miRNAs and/or miRNA inhibitors are used in library screening assays.

Abstract: Provided are a primer set for amplifying target sequence(s) of antibiotic-resistant bacterial species, a probe or probe set specifically hybridizing with target sequence(s) of antibiotic-resistant bacterial species, a microarray immobilized with the probe or probe set, a kit comprising the primer set and a method of detecting at least one antibiotic-resistant bacterial species using the probe or probe set.

Abstract: The invention provides methods and compositions for screening polypeptide libraries that include variants comprising unnatural amino acids. In addition, the invention provides vector packaging systems and methods for packaging a nucleic acid in a vector.

Abstract: In one aspect, the invention provides composition and methods for the diagnosis, prognosis and treatment of tumors and cancers, e.g., brain cancers. In one aspect, the invention provides compositions and methods for inhibiting the growth, proliferation, differentiation and/or survival of a neural stem cell or a cancer cell, or progenitor stem cell thereof. In one aspect, the invention provides compositions and methods for identifying the genetic profile of a brain cancer cell or a self-renewing neural cancer stem cell. In one aspect, the invention provides methods employing these profiles to identify compounds that inhibit tumor growth.

Abstract: The present invention provides methods for the assessment, diagnosis, or prognosis of asthma including methods for providing an assessment, diagnosis, or prognosis comprising the step of exposing a sample derived from a patient to an allergen in vitro. The present invention also provides methods for selecting, as well as evaluating the effectiveness of, asthma treatments.

Abstract: To provide a method for selecting a marker gene useful for cancer classification; a method for classifying cancer using the gene; a method for detecting cancer; a kit usable for the classification method or detection method; and a DNA array carrying the gene. According to the present invention, there can be obtained a gene, wherein expression of the above gene is altered independently from genes each of which expression is altered specifically during cell proliferation and expression level of the above gene is specifically altered depending on every type of cancer samples to be tested, whereby the classification or detection of cancer can be carried out conveniently and quickly without giving surgical treatment. Therefore, the present invention is useful for the diagnosis, the treatment, and the like of cancer.

Abstract: The invention relates to products and processes for determining or predicting sporting performance, ability or aptitude of horses and other performance animals through the study of nucleotide sequence variants, genetic types or profiles, in particular the study of mitochondrial sequence variants. The invention is useful in the horseracing industry.

Abstract: The invention provides methods and compositions useful for detecting mutations in c-met in lung cancer cells.

Abstract: This invention provides a series of low-copy number plasmids comprising restriction endonuclease recognition sites useful for cloning at least three different genes or operons, each flanked by a terminator sequence, the plasmids containing variants of glucose isomerase promoters for varying levels of protein expression. The materials and methods are useful for genetic engineering in microorganisms, especially where multiple genetic insertions are sought.

Abstract: The present invention relates to functionalized porous carriers which comprise a material having at least one porous surface, nanoparticles having molecule-specific recognition sites being present in the pores of the material surface, and to a process for producing functionalized porous carriers. The invention further relates to functional elements produced using the functionalized carriers, such as microtiter plates, microarrays and flow devices, and also to uses of the functionalized carriers and functional elements.

Abstract: The present invention relates to a method of ensuring the effectiveness of the extraction workup from a biological sample of nucleic acid. The inventive method is able to distinguish between possible defects in the extraction of nucleic acid from a sample and possible defects in a subsequent amplification step. The present invention also relates to a packaged array for extracting nucleic acid from a biological sample.

Abstract: The present invention provides methods and compositions for performing ordered multi-step syntheses by nucleic acid-mediated chemistry. This approach provides increased yields, and control over the preparation, of products produced via sequential, multi-step syntheses in a single reaction vessel.

Abstract: The present invention relates to immunoglobulin new antigen receptors (IgNARs) from fish and uses thereof. In particular, the present invention relates to modified IgNAR variable domains and to domains from members of the immunoglobulin superfamily that have been modified to include structural features derived from IgNAR variable domains.

Abstract: A process for constructing an artificial coding sequence is provided. The process comprises providing an enzyme adapted to ligate DNA duplexes containing selected codons into multimers that preserve the reading frame of those codons in a reaction facilitated by the presence of a condensing agent, such as polyethylene glycol. These open reading frames may be useful for expressing proteins with a restricted amino acid content.

Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.

Abstract: The present invention provides a microarray for detecting a genotype at a polymorphic site in a plurality of nucleic acid samples, comprising a first set of nucleic acid fragments derived from the samples and a second set of nucleic acid fragments derived from a plurality of references immobilized thereon. The invention also provides a microarray comprising a set of nucleic acid fragments immobilized on the surface of the microarray, wherein the nucleic acid fragments are derived from the samples by amplifying a region in the sample containing the polymorphism through asymmetric PCR amplification. Methods of using and making the microarrays are also provided.

Abstract: An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array.

Abstract: The present invention provides sequences and reagents for preparing microarrays with internal controls. Specifically, the present invention defines and provides sequences that are not present in the hybridizing mRNA or cDNA, and therefore can be used both as hybridization controls and for inter-spot normalization.

Abstract: The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5? end to prohibit degradation by a 5?-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface.

Abstract: The present invention relates broadly to compositions and methods for performing nucleic acid analysis. In particular the invention relates to a universal oligonucleotide probe set and a hybridization matrix or array for performing analysis of nucleic acids from any source. The oligonucleotide matrix of the present invention provides up to approximately 1018 different oligonucleotides thus being sensitive enough to provide unprecedented capacity and sensitivity.

Abstract: The invention relates to a method for synthesizing templated molecules attached to the templated which directed the synthesis thereof. The method involves a template, a scaffold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The scaffold functional entity and the functional entity of the building block are both provided with complementary dimerization domains allowing the functional entities to come into close proximity when the complementary domains interact with to each other. The method may be used for generating libraries of templated molecules which may be selected for biological activity.

Abstract: Disclosed for instance, are methods suitable for the detection, identification and/or quantitation of nucleic acid target sequences using probes. Suitable probes include those consisting of peptide nucleic acid (PNA) or locked nucleic add (LNA) units. Binding of the probes to adjacent target sequences results in fluorescent quenching. Analysis of changes in the fluorescent signal is used to detect, identify or quantitate a target sequence in a sample. The invention is more specifically directed to methods for improving the sensitivity, specificity and/or reliability of diagnostic tests using suitable probes. It is particularly well-suited for real-time PCR and related amplification reaction.

Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Abstract: The invention relates to a method for manufacturing a recombinant polyclonal protein composition, in particular a recombinant polyclonal antibody composition. The method comprises obtaining a collection of cells transfected with a library of variant nucleic acid sequences, wherein each call in the collection is transfected with and capable of expressing one member of the library, which encodes a distinct member of a polyclonal protein that binds a particular antigen and which is located at the same single site in the genome of individual cells in said collection, wherein said nucleic acid sequence is not naturally associated with said cell in the collection. The cells are cultured under suitable conditions for expression of the polyclonal protein, which is obtained from the cells or culture supernatant. The nucleic acid sequence id introduced into the cells by transfection with a library of vectors for site-specific integration.

Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Abstract: A sensor chip and detection device are disclosed. The sensor chip includes a substrate, at least a portion of which is covered by a metal nanoparticle film; a first nucleic acid molecule that is characterized by being able to (i) self-anneal into a hairpin conformation and (ii) hybridize specifically to a target nucleic acid molecule, the first nucleic acid molecule having first and second ends, which first end is tethered to the metal nanoparticle film; and a first fluorophore bound to the second end of the first nucleic molecule. When the first nucleic acid molecule is in the hairpin conformation, the metal nanoparticle film substantially quenches fluorescent emissions by the first fluorophore, and when the first nucleic acid molecule is in a non-hairpin conformation fluorescent emissions by the first fluorophore are surface plasmon-enhanced.

Abstract: The invention provides an artificial protein for quantitative analysis of the proteome of a sample, cell or organism, comprising at least two consecutive peptides linked by a cleavage sequence for separating the peptides; a singular marker on one or more peptide for determination of the absolute amount of this fragment; and N-terminal and C-terminal extensions for protection of the peptides; wherein each peptide represents one single protein of the sample, cell or organism and each peptide is in a defined stoichiometry. The invention further provides a collection of peptides, a vector and a kit comprising the artificial protein and a method for quantitative analysis of the proteome.

Abstract: This invention relates generally to biosensor technology, and pertains more particularly to novel multifunctional biosensors based on ordered arrays of metallic, semiconductors and magnetic nano-islands for medical, biological, biochemical, chemical and environmental applications.

Abstract: The present invention provides methods and compositions for predicting patient responses to cancer treatment using hypoxia gene signatures. These methods can comprise measuring in a biological sample from a patient the levels of gene expression of a group of the genes designated herein. The present invention also provides for microarrays that can detect expression from a group of genes.

Abstract: Method for identifying myeloid or plasmacytoid dendritic cells provided by a mammal, stimulated or unstimulated, comprising the steps of: a) preparing a cell sample; b) contracting the cell sample myeloid or plasmacytoid dendritic cells to form a complex; c) detecting the complex; characterized in that the phosphatase is the Receptor type Tyrosine Phosphatase Gamma Protein (PTPRG), acting as a specific marker of said dendritic cells, and in that the compound is a polypeptide capable of selectively bind to the PTPRG or to a fragment thereof or to a oligonucleotide complementary to a PTPRG mRNA logonucleotide in such a manner as to allow the selective recognizing of the dendritic cells in the cell sample.

Abstract: Variations in certain genomic sequences useful as genetic markers of Sudden Cardiac Death (“SCD”), or Sudden Cardiac Arrest (“SCA”) risk, are described. Novel diagnostic kits and methods employing these genetic markers are used in assessing the risk of SCD, or SCA. Methods of distinguishing patients having an increased susceptibility to SCD, or SCA, through use of these markers, alone or in combination with other markers, are also provided. Further, methods of assessing the need for an Implantable Cardio Defibrillators (“ICD”) in a patient are taught.

Abstract: There is provided a first method of preparing a genome library in which PCR is carried out with the use of genomic DNA of target biological species per se or fragment thereof as a direct template and with the use of random primer or one type of primer of specified sequence so as to effect genome amplification, thereby obtaining a genuine library. There is further provided a second method of preparing a genome library in which genome of target biological species is pretreated and thereafter PCR is carried out with the use of one type of primer of inherent sequence so as to effect genome amplification, thereby obtaining a genome library. In both of the methods, a genome library can be prepared conveniently from a minute amount of sample.

Abstract: The present invention is directed to the use of the maize Ac/Ds transposable elements in vertebrates.

Abstract: The present invention provides methods for diagnosis and prognosis of cancer stem cells (CSC) using expression analysis of one or more groups of genes, and a combination of expression analysis from a biological sample from the subject. The methods of the invention provide a method for accuracy detecting cancer stem cells in a population of cancer cells. The invention also provides methods and kits for diagnosis and prognosis of cancer in a subject using cancer stem cell biomarker expression analysis.

Abstract: The invention relates to methods of making modular chimeric protein expression products and compositions utilized in the methods. In particular, the invention relates to sequential, directional cloning of polynucleotides encoding polypeptide modules. Each clonable element or module contains an open reading frame of interest flanked by predetermined restriction sites. The methods include using modules and vectors containing these modules as starting materials for recombinant DNA techniques. One advantage of the invention is that it allows for many variations of fusion proteins to be made quickly and easily without needing to design and evaluate each subsequent cloning step.

Abstract: Disclosed herein are methods and compositions useful for identifying therapies likely to confer optimal clinical benefit for patients with cancer.

Abstract: Provided are methods and oligonucleotides useful as primers and templates for internal controls designed for use in Real Time Reverse Transcriptase Polymerase Chain Reactions. Use of the present methods and oligonucleotides allows validation of assay parameters and of the results that an assay set.

Abstract: The present invention relates to a gene and/or protein expression based method of predicting response to platinum based chemotherapy for lung cancer patients, as well as a method of predicting prognosis of survival based on protein expression and type of lung cancer. The invention also provides novel targets for screening candidate anti-cancer agents.

Abstract: The invention relates to an arrangement of proteins containing at least one cDNA-expression library and to the use thereof as a protein-biochip, in particular for validating binding agents and protein binding agents and to a method for determining in a simultaneous manner quantitative variables.

Abstract: Methods arrays and systems that facilitate contig assembly during nucleic acid sequencing are provided. Geographical locations of analyte molecules on an array are correlated with subsequence relationships within larger nucleic acids.

Abstract: A template-based system enables the assembly of macromolecules and nanostructures. The template system comprises a plurality of single strand DNA molecules which are substantially parallel, substantially inline each from one end, and substantially equally spaced apart, wherein each DNA molecule has a distinguishable length and a known sequence. The system can be used for the precise, accurate, and efficient synthesis of peptides, proteins and enzymes.

Abstract: The present invention relates to methods for multiplex detection and quantification of target nucleic acid sequences in a sample comprising the steps of: (i) providing a solid support having immobilized thereon an array of detector oligonucleotides, wherein said array of detector oligonucleotides is designed by random selection of non-eukaryotic genomic sequences followed by random selection of oligonucleotide sequences and subsequent conversion of these oligonucleotide sequences such that these are composed of only three types of nucleotides; (ii) providing a sample having added thereto a fixed amount of control nucleic acid of known sequence; (iii) contacting said sample with at least two probes that hybridise to adjacent sites of a target sequence under conditions favouring hybridisation between the sample nucleic acids and the said at least two probes, wherein, a) a first probe is composed of a 5? end sequence part for hybridisation to a PCR primer and a 3? end sequence part for hybridisation to the targe

Abstract: The present invention provides for certain polynucleotide sequences that have been correlated to AMD. These polynucleotides are useful as diagnostics, and are preferably used to fabricate an array, useful for screening patient samples. The array is used as part of a laboratory information management system, to store and process additional patient information in addition to the patient's genomic profile. As described herein, the system provides an assessment of the patient's risk for developing AMD, risk for disease progression, and the likelihood of disease prevention based on patient controllable factors.

Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing selective capture of defined molecules. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.