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 amplification procedures. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

Abstract: The present invention makes known an array of nucleotididc sequences for rapidly and simultaneously identifying the presence of certain genes that codify proteins with activities relevant in biotechnology, present in a microbiological sample, and the method for using this array in the identification of the said genes. Specifically, genes that codify for proteins relevant in Biofilm formation, in CO2 fixation, in Energetic metabolism, for chemiotaxis and mobility, in iron oxidization, in nitrogen metabolism, in Sulfur assimilation, and in oxidation/reduction of sulfide compounds. This array of nucleotidic sequences is presented as a useful tool in biotechnology in all cases requiring an evaluation of the quality of a microbiological community.

Abstract: The present invention provides a versatile and sensitive method for studying interaction of two peptides or polypeptides A and B within the cytoplasm of a host cell. The method is based on the use of two distinct chimeric polypeptides. The first chimeric polypeptide containing an aggregation domain fused to a polypeptide A and the second one containing a phenotype-associated functional domain fused to a second polypeptide B. When these chimeric polypeptides are co-expressed within a host cell allowing aggregation of the aggregation domain, the phenotype of the host cell depends on the entrapment of the phenotype-associated functional domain which only occurs when A and B interact with each other.

Abstract: A test apparatus is for testing a DNA substrate on which a plurality of DNA fragments for testing are arranged, wherein absolute precision is not required. A substrate is provided on which a plurality of biomolecule spots containing a group of biomolecules (e.g., DNA, etc.) of a specific type are formed, where the pattern or position of the DNA spot is changed depending on specific data so that information of the specific data is recorded on the substrate.

Abstract: The invention provides a method of diagnosing carcinoma in a patient, the method comprising providing a sample of colorectal cells from a human patient and analyzing the sample for CXCL12 hypermethylation.

Abstract: This invention relates to novel proteins (herein termed INSP141, INSP142, INSP143, and INSP144), herein identified as anthrax receptor-like proteins containing von Willebrand factor A (vWFA) and Anthrax receptor extracellular (ANT_IG) domains and to the use of these proteins and nucleic acid sequences from the encoding genes in the diagnosis, prevention and treatment of disease.

Abstract: The invention provides for compositions and methods for predicting an individual's responsitivity to cancer treatments and methods of treating cancer. In certain embodiments, the invention provides compositions and methods for predicting an individual's responsitivity to chemotherapeutics, including salvage agents, to treat cancers such as ovarian cancer. The invention also provides reagents, such as DNA microarrays, software and computer systems useful for personalizing cancer treatments, and provides methods of conducting a diagnostic business for personalizing cancer treatments.

Abstract: Detection of epigenetic alteration, especially methylation, of a gene or a combination of genes, preferably in a perinatal tissue sample such as umbilical cord, for predicting diverse phenotypic characteristics such as propensity for obesity, altered body composition, impaired cognition, low bone mineral content, neuro-behavioural problems and altered cardiovascular structure and function occurring in an individual.

Abstract: Arrays of HLA Class I oligonucleotide probes on a solid support are provided, wherein the probes are sufficient to represent at least 80% of the known polymorphisms in exons 2 and 3 of the HLA Class I locus.

Abstract: A method of diagnosing melanoma and/or monitoring melanoma progression, in particular for determining whether the melanoma is likely to have metastatic capabilities, in a subject includes the steps of in a test sample determining the methylation status of FABP5 wherein methylation of the gene indicates a positive diagnosis of melanoma and/or increased methylation of the gene indicates the progression of melanoma. Methods of monitoring melanoma progression may also incorporate measuring the expression levels of FABP5, with low levels of expression indicating a positive diagnosis of melanoma and/or lower levels of expression being indicative of progression of melanoma. Methods of treating melanoma in a subject comprise administering a therapeutically effective amount of a DNA methyltransferase inhibitor or a histone deacetylase inhibitor to the subject such that expression of FABP5 is increased.

Abstract: Methods for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In some embodiments of the subject methods, a plurality of sequence-specific primers are employed to enzymatically generate a set of labeled target nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and can be used, for example, in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

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 present invention is directed to the preparation and use of a collection of antibody heavy chain complementarity determining region 3 (HCDR3) members, where diversity of the collection is a function of the length of the HCDR3 members. The diversity of the collection of HCDR3 regions substantially represents the natural amino acid distribution of HCDR3 in the human repertoire. This natural amino acid distribution can be represented by biasing the complete random distribution of amino acids, accordingly, in the HCDR3 encoding DNA sequence by using trinucleotide mutagenesis (TRIM) technology. A collection of HCDR3 members of the invention each can be comprised within a variable region of an antibody (or fragment thereof) to form a library of synthetic antibodies or antibody fragments. The invention also provides nucleic acid molecules encoding such diverse collection and methods of making and using the same.

Abstract: The present invention relates to a gene discovery system and gene expression systems specific for genes encoding ARE-containing mRNAs. In one aspect, the present invention relates to computational methods of selecting coding sequences of ARE-genes from databases using a one or more ARE search sequences. The ARE search sequences are from 10 to 80 nucleotides in length and comprise a sequence which is encompassed by one of the following two sequences: (a) WU/T(AU/TU/TU/TA)TWWW, SEQ ID NO. 1, wherein none or one of the nucleotides outside of the parenthesis is replaced by a different nucleotide, and wherein W represents A, U, or T; and (b) U/T(AU/TU/T/U/T)n, SEQ ID NO. 2 wherein n indicates that the search sequence comprises from 3 to 12 of the tetrameric sequences contained within the parenthesis. The method comprises extracting from the databases, those nucleic acids whose protein coding sequences are upstream and contiguous with a 3? untranslated region (UTR) that comprises one of the ARE search sequences.

Abstract: Methods for diagnosing the presence or absence of a genetic disorder in a patient are provided, wherein the genetic disorder is associated with a chromosomal abnormality at 1q41q42 and/or 16p11.2p12.2, and wherein the genetic disorder is not Fryns syndrome or congenital diaphragmatic hernia (CDH). Materials, such as microarrays for use in microarray CGH, and kits for use in such methods are also provided.

Abstract: The present invention relates to novel methods for the quantitative detection of molecules in an array. In particular, the present invention relates to methods and apparatuses for producing a frameless array. In another embodiment, the present invention relates to a composition comprising nitrocellulose that is useful of producing a frameless array. In another embodiment, the present invention relates to a method for detecting a molecular interaction. In yet another embodiment, the present invention relates to kits useful for practicing the methods and apparatuses of the present invention. The present invention provides improved methods and apparatuses for the high throughput analysis of molecular interactions and quantitative detection.

Abstract: The present invention provides DNA libraries, libraries of viral clones and libraries of infectious viral particles and methods of generating and screening these libraries.

Abstract: In some embodiments, the present disclosure provides methods of making a mixture of nucleic acid molecules, the methods comprising the steps of: synthesizing on a substrate a population of nucleic acid molecules wherein each synthesized nucleic acid molecule comprises a substrate-attached proximal nucleic acid molecule, a distal nucleic acid molecule, and a cleavable linker linking the proximal nucleic acid molecule to the distal nucleic acid molecule, and harvesting distal nucleic acid molecules from the substrate by cleaving the cleavable linker under conditions that do not release the proximal nucleic acid molecule. Related compositions and kits are also provided.

Abstract: Compilations of nucleic acids, articles of manufacture which are surfaces comprising multiple blocks of arrays comprising such compilations, methods of use of the compilations and arrays for detection of chromosomal disorders, such as a chromosomal aneuploidies, deletions, amplifications, and diagnosis and prognosis of syndromes associated with a contiguous gene abnormality and kits are provided.

Abstract: The invention relates to small single stranded RNAs and analogs thereof (collectively “piRNA” herein), compositions comprising such piRNAs, and their uses in regulating target gene expression or as markers for certain disease states.

Abstract: The invention provides a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, characterised in that the cleavable linker contains a moiety selected from the group comprising: Formula (I) (wherein X is selected from the group comprising O, S, NH and NQ wherein Q is a C1-10 substituted or unsubstituted alkyl group, Y is selected from the group comprising O, S, NH and N(allyl). T is hydrogen or a C1-10 substituted or unsubstituted alkyl group and * indicates where the moiety is connected to the remainder of the nucleotide or nucleoside).

Abstract: This present invention compositions and methods of treating cancer and methods of accessing/monitoring the responsiveness of a cancer cell to a therapeutic compound.

Abstract: The present disclosure provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles typically comprise steps of extension, ligation, and cleavage. In certain embodiments, the methods make use of extension probes containing phosphorothiolate linkages and agents capable of cleaving such linkages. Methods of determining information about a sequence using at least two distinguishably labeled probe families are provided, as are methods of performing multiple sequencing reactions on a single template. Automated sequencing systems, flow cells, image processing methods, and computer-readable media that store computer-executable instructions and/or sequence information that can be used in accordance with such methods are also provided. In certain embodiments, blocking oligonucleotides are provided to facilitate sequencing using disclosed methods.

Abstract: A first embodiment is a non-small cell lung cancer recurrence prognosticator comprising a detection mechanism consisting a 35-gene signature. A second embodiment is a non-small cell lung cancer tumor stage prognosticator comprising a detection mechanism consisting an 11-gene signature. A third embodiment is a non-small cell lung cancer differentiation prognosticator comprising a detection mechanism consisting an 18-gene signature.

Abstract: The invention provides isolated and recombinant phytase enzymes. In one aspect, the phytases are produced by modification of the wild type appA of E. coli. The enzyme can be produced from recombinant host cells. The phytases of the invention can be used to aid in the digestion of phytate where desired. In particular, the phytases of the invention can be used in foodstuffs to improve the feeding value of phytate rich ingredients. The phytases of the invention can be thermotolerant and/or thermostable. Also provided are methods for obtaining a variant polynucleotide encoding a phytase and for obtaining a phytase with thermostability or thermotolerant at high or low temperatures.

Abstract: A method for diagnosing the presence of hereditary spastic paraplegia (HSP) or predicting the risk of developing HSP in a human subject, comprising detecting the presence or absence of a defect in a gene encoding a polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19), in a nucleic acid sample of the subject, whereby the detection of the defect is indicative that the subject has or is at risk of developing HSP.

Abstract: The present invention provides improved methods for generating fluorescent aptamer polynucleotides, novel polynucleotides, and methods for use thereof.

Abstract: A method of detecting cardiac arrhythmia in a patient is described. This method involves determining whether there is a mutation in the nucleotide sequence, the amino acid sequence, or both, of connexin40 obtained from a patient. The mutation may be localized within the transmembrane domain of connexin40. Furthermore, there is described a method of identifying a compound for the treatment of cardiac arrhythmia. This method involves providing a cell culture that is characterized by having impaired intracellular trafficking, impaired electrical coupling, reduced gap junction plaque formation, reduced intracellular coupling, or a combination thereof, when compared to a wild-type cell. A compound is added to the cell culture, and restoration of intracellular trafficking, electrical coupling, gap junction plaque formation, intracellular coupling, or a combination thereof, is monitored.

Abstract: A sensor chip that includes: a fluorescence quenching surface; a nucleic acid probe that contains first and second ends with the first end bound to the fluorescence quenching surface, and is characterized by being able to self-anneal into a hairpin conformation; and a first fluorophore bound to the second end of the first nucleic acid molecule. When the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface 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 fluorophore are substantially free of quenching by the fluorescence quenching surface. Various nucleic acid probes, methods of making the sensor chip, biological sensor devices that contain the sensor chip, and their methods of use are also disclosed.

Abstract: The present invention provides a tool for analysis of expression of Macaca fascicularis gene. The present invention provides a Macaca fascicularis gene expression analysis tool containing a set of nucleic acids containing base sequences the same or substantially the same as two or more base sequences selected from the group consisting of the base sequences shown by SEQ ID NOs: 1-14, or partial sequences thereof, and a method of analyzing the expression of Macaca fascicularis gene, including measuring a gene transcription product in a Macaca fascicularis sample using the tool.

Abstract: The present invention relates to an instrument, a method and a kit for detecting a microorganism contaminating a subject test sample, which enables one to quickly and accurately identify the microorganism with an easy operation. The instrument for detecting a microorganism according to the present invention relates to a microarray type instrument in which oligonucleotides prepared based on nucleotide sequences specific to the species and genus to which the subject microorganism belongs have been immobilized onto a surface of a substrate. Based on the presence or absence of hybridization of the probes prepared from the test sample with the oligonucleotides immobilized onto the surface of the substrate, the present invention makes it possible to detect and/or identify the microorganism in the test sample easily, quickly and accurately.

Abstract: A method of identifying a compound capable of reducing or preventing prolonged sensory neuron hyper-excitability comprising the steps of: (a) administering the compound to an experimental non-human animal having prolonged sensory neuron hyper-excitability; (b) generating an expression profile of the genes modulated in the Nodose Ganglia (NG) of the animal of step (a); (c) comparing the expression profile obtained in (b) with the expression profile of a corresponding panel of genes expressed in the NG of an experimental non-human animal having no prolonged sensory neuron hyper-excitability; wherein a positive correlation of the expression profiles is indicative that the compound is capable of reducing or preventing prolonged sensory neuron hyper-excitability in NG.

Abstract: The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted CD84-like polypeptide. These polynucleotides comprise nucleic acid sequences isolated from cDNA library from human spleen (Hyseq clone identification numbers 2938352 (SEQ ID NO: 1)). Other aspects of the invention include vectors containing processes for producing novel human secreted CD84-like polypeptides, and antibodies specific for such polypeptides.

Abstract: The present invention relates to a non-PCR (polymerase chain reaction) process, particularly a transcription-based amplification method, for amplifying and cloning sequences containing a variable domain sequence such as an immunoglobulin variable domain sequence from the immunological gene repertoire. The present invention contemplates the expression of antibody library in either in an in vivo expression vector or in an in vitro transcription/translation system. Isolation of a gene coding for a receptor having the ability to bind a preselected ligand and receptors produced by the gene isolated by the method is also contemplated.

Abstract: Arrays and substrates comprising a material, in particular capture agents and/or detectable targets, attached to the substrates along substantially parallel lines forming a barcoded pattern and related methods and systems.

Abstract: The present invention provides new methods for the assessment of cancer risk in the general population. These methods utilize particular alleles of in multiple selected genes to identify individuals with increased or decreased risk of breast cancer. In addition, personal history measures such as age and family history are used to further refine the analysis. Using such methods, it is possible to reallocate healthcare costs in cancer screening to patient subpopulations at increased cancer risk. It also permits identification of candidates for cancer prophylactic treatment.

Abstract: The present invention relates to surface modifications and linker attachments. For example, the present invention provides surface modification and linker chemistry that facilitates manufacture and use of microarrays, including nucleic acid and protein microarrays. The present invention also relates to array spotting through non-aqueous liquids.

Abstract: By a computer search for upstream promoter elements (DSE, PSE) typical of small nuclear RNA (snRNA) genes, we have identified a number of previously unrecognized, putative transcription units whose predicted products are novel noncoding RNAs with homology to protein-coding genes. By elucidating the function of one of them, we provide evidence for the existence of a sense/antisense-based gene regulation network where part of the Pol III transcriptome could control its Pol II counterpart.

Abstract: The present invention relates to a gene discovery system and gene expression systems specific for genes encoding ARE-containing mRNAs. In one aspect, the present invention relates to computational methods of selecting coding sequences of ARE-genes from databases using aone or more ARE search sequences. The ARE search sequences are from 10 to 80 nucleotides in length and comprise a sequence which is encompassed by one of the following two sequences: (a) WU/T(AU/TU/TU/TA)TWWW, SEQ ID NO. 1, wherein none or one of the nucleotides outside of the parenthesis is replaced by a different nucleotide, and wherein W represents A, U. or T; and (b) U/T(AU/TU/T/U/T)n, SEQ ID NO. 2, wherein n indicates that the search sequence comprises from 3 to 12 of the tetrameric sequences contained within the parenthesis. The method comprises extracting from the databases, those nucleic acids whose protein coding sequences are upstream and contiguous with a 3?untranslated region (UTR) that comprises one of the ARE search sequences.

Abstract: The invention relates to a method for manufacturing an anti-RhD recombinant polyclonal antibody composition (anti-RhD rpAb). The method comprises obtaining a collection of cells transfected with a library of anti-RhD antibody expression vectors, wherein each cell in the collection is capable of expressing from a VH and VL comprising nucleic acid segment, one member of the library, which encodes a distinct member of anti-RhD recombinant polyclonal antibody composition and which is located at the same site in the genome of individual cells in said collection. The cells are cultured under suitable conditions for expression of the recombinant polyclonal antibody, which is obtained from the cells or culture supernatant. The nucleic acid segments encoding the anti-RhD rpAb is introduced into the cells by transfection with a library of vectors for site-specific integration.

Abstract: The present invention provides self-assembling, finite nucleic acid tiling arrays, and methods for their synthesis and use, which overcome a major hurdle in self-assembled DNA nanostructures, and therefore have numerous potential applications for nanofabrication of complex structures and useful devices, as further disclosed herein.

Abstract: The invention includes method of determining if a subject has a genetic predisposition to clinically diagnosed schizophrenia (SZ), schizotypal personality disorder (SPD), and/or schizoaffective disorder (SD).

Abstract: The present invention provides B7-Like (B7-L) polypeptides and nucleic acid molecules encoding the same. The invention also provides selective binding agents, vectors, host cells, and methods for producing B7-L polypeptides. The invention further provides pharmaceutical compositions and methods for the diagnosis, treatment, amelioration, and/or prevention of diseases, disorders, and conditions associated with B7-L polypeptides.

Abstract: Aspects of the invention provide compositions and methods for displaying engineered polypeptides on a cell surface. According to aspects of the invention, immobilized polypeptides can be screened to identify one or more variants having one or more functional or structural properties of interest. Aspects of the invention provide composition and methods for producing engineered protein or protein variants having a functional or a structural property of interest.

Abstract: The present invention is directed to novel nucleic acid molecules which include a region complementary to a target gene and one or more self-complementary regions, and the use of such nucleic acid molecules and compositions comprising the same to modulate gene expression and treat a variety of diseases and infections.

Abstract: This invention relates, in part, to unique and newly identified genetic polynucleotides involved in the process of bone remodeling; variants and derivatives of the polynucleotides and corresponding polypeptides; uses of polynucleotides, polypeptides, variants and derivatives; and methods and compositions for the amelioration of symptoms caused by bone remodeling disorders. Disclosed in particular are, the isolation and identification of polynucleotides, polypeptides, variants and derivatives involved in osteoclast activity, validation of the identified polynucleotides for their potential as therapeutic targets and use of the polynucleotides, polypeptides, variants and derivatives for the amelioration of disease states and research purposes.

Abstract: The invention provides molecular switches which couple external signals to functionality, and combinatorial methods of making and using the same involving circular permutation of nucleic acid and amino acid sequences. The switches according to the invention can be used, for example, to regulate gene transcription, target drug delivery to specific cells, transport drugs intracellularly, control drug release, provide conditionally active proteins, perform metabolic engineering, and modulate cell signaling pathways. Libraries comprising the switches, expression vectors and host cells for expressing the switches are also provided.

Abstract: The invention provides methods and compositions useful for detecting autoimmune disorders.

Abstract: The present invention is directed to methods for ameliorating reproductive disorders. More specifically, the present invention describes methods and compositions for using IL-17 in the treatment of various infertility-related defects.

Abstract: The present invention relates to compositions and methods for treating, characterizing, and diagnosing cancer. In particular, the present invention provides gene expression profiles associated with solid tumor stem cells, as well as novel stem cell cancer gene signatures useful for the diagnosis, characterization, prognosis and treatment of solid tumor stem cells.