Abstract: The invention relates to a method of producing an oligonucleotide library comprising a plurality of oligonucleotides, each oligonucleotide in the library having at least one predetermined position, a randomisation codon selected from a defined group of codons, the codons within said defined group coding for different amino acids. Vector, host cells containing such libraries and kits for the production of such libraries are also provided.

Abstract: Provided are an isolated nucleolar protein having an amino acid sequence of NCBI GenBank Accession No. XP_033371, a method of diagnosing colorectal cancer in an individual, including measuring an expression level of a protein having an amino acid sequence of NCBI GenBank Accession No. XP_033371 in the individual, and a polynucleotide for diagnosis or treatment of colorectal cancer including at least 10 contiguous nucleotides of a nucleotide sequence selected from the group consisting of nucleotide sequences of SEQ ID NOS: 1-5 and including a nucleotide at position 101 of the nucleotide sequence, or a complementary polynucleotide thereof.

Abstract: The present invention relates to novel methodologies for performing multiplexed assays for biological molecules such as proteins and nucleic acids. In particular, the present invention provides multiplexed assays using precipitating reagents and optically clear nitrocellulose-coated solid supports.

Abstract: A genetic locus and corresponding family of proteins associated with regulation of immune function and cell survival are provided. These genes encode cell surface molecules with conserved IgV and mucin domains. The locus comprising the TIM family is genetically associated with immune dysfunction, including asthma. Furthermore, the TIM gene family is located within a region of human chromosome 5 that is commonly deleted in malignancies and myelodysplastic syndrome. Polymorphisms in the gene sequences are associated with the development of airway hyperreactivity and allergic inflammation, and T cell production of IL-4 and IL-13. The proteins include the human hepatitis A cellular receptor, hHAVcr-1.

Abstract: The present invention provides an isolated polynucleotide comprising at least one polymorphic nucleotide sequence, for example, the major alleles of the SNPs described as rs12583006, rs1224141, and rs1248930 and diagnostic assays for detecting the presence of these polymorphism associated with a condition associated with BLyS activity, such as hematological malignancy including B cell malignancies. The diagnostic assays are useful in predicting an individual's likelihood of developing a condition associated with BLyS activity, such as hematological malignancies, and for methods for treating an individual clinically diagnosed with a condition associated with BLyS activity, such as prediction of a patient's likelihood to respond to a specific drug treatment. The invention also provides an array of nucleic acid molecules immobilized on a solid surface, where at least one of the nucleic acid molecules comprises a BLyS polymorphic nucleic acid molecule.

Abstract: Single nucleotide polymorphic sites at positions 3117, 12195, 13244, 13319, and 13516 of the bovine STAT5 gene are associated with improved fertilization rate and/or improved embryo survival rate. Also disclosed are nucleic acid molecules, kits, methods of genotyping and marker assisted bovine breeding methods.

Abstract: An article such as a biomolecular detector or biosensor having a nonfouling surface thereon includes:(a) a substrate having a surface portion; (b) a linking layer on the surface portion; and (c) a polymer layer formed on the linking layer; and (d) a first member of a specific binding pair (e.g., a protein, peptide, antibody, nucleic acid, etc.) bound to the polymer layer. Methods of making and using the articles are also described.

Abstract: The present invention is concerned with improvements to methods of imaging nucleotides incorporated into polynucleotides and in particular with improved methods of determining the sequence of template nucleic acid molecules using multiple cycle nucleic acid “sequencing-by-synthesis” reactions.

Abstract: The present invention provides kits and microarrays containing primer pairs for amplifying drug resistance genes and/or probes for detection of drug resistance genes. Also provided are methods of detecting drug resistance genes using kits and microarrays described herein.

Abstract: The present invention provides methods and devices for making new and inexpensive miniarrays suitable for gene expression analysis. Also provided herein are methods of diagnosis for specific tissue or condition using specialized diagnostic miniarrays that exhibit specific visual pattern as diagnostic readout.

Abstract: The invention relates to polypeptides and polynucleotides associated with trophoblast cell death, differentiation, invasion, and/or cell fusion and turnover, and uses of same in the prevention, diagnosis and treatment of conditions requiring regulation of trophoblast cell death, differentiation, invasion, and/or cell fusion and turnover. In particular aspects, diagnostic methods are disclosed for evaluating conditions such as preeclampsia utilizing matador polypeptides and polynucleotides encoding same.

Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.

Abstract: Methods for detection of variant alleles are disclosed. In preferred aspects variants are detected by hybridization patterns to arrays of probes that are contain a single mismatch to a reference sequence, thus reducing the number of probes needed for resequencing by hybridization. The target capture method used is Target Amplification by Capture and Ligation (TACL), and is capable of amplifying many thousands of loci together. Mismatch Repair Detection (MRD) is used as an allele enrichment method to efficiently sort variant and non-variant alleles in thousands of loci simultaneously.

Abstract: Compositions and methods for the autonomous in vitro evolution of molecules having specific properties, employing one-pot continuous evolution are disclosed.

Abstract: The invention relates to the field of medical diagnostics. More specifically, the invention relates to methods to diagnose or screen for inflammatory condition or disease, including auto-inflammatory disease and affective disorder, in a subject, preferably a human subject, by assaying for a marker for an inflammatory disease. Provided is a method to diagnose, screen for or predict the development of an affective disorder (AD), preferably bipolar disorder (BP), in a subject, said method comprising determining the level of at least one, preferably at least two, more preferably at least three, most preferred at least four, AD-specific gene product(s) in a biological sample isolated from said subject, preferably peripheral blood monocytes, wherein said gene is selected from the group comprising Syntaxin1a, FCAR, SDR1, PTPN7, FABP5 and CD9.

Abstract: The present invention provides a method for assessing the prognosis of Ewing's Sarcoma patients comprising determining the expression pattern of a defined set of genes in tumor material obtained from said patients, and assigning said expression pattern to either a good prognosis or poor prognosis group.

Abstract: The object of this invention is to provide a substrate that enables quantification of target substances as absolute values at a single cell level, and a method for such quantification. The substrate according to this invention is characterized in that it comprises a concentration gradient spotting portion comprising fragments having binding property with probe and having plural concentration gradients, and a specimen setting portion for setting specimen containing target substance having binding property with said probe.

Abstract: Disclosed herein are methods of destabilizing double-stranded nucleic acid hybridization using an enzyme comprising DNA N-glycosylase activity. Also disclosed herein is the detection of a double-stranded target DNA wherein the hybridization of duplex strands has been at least partially disrupted thereby permitting invasion of a probe strand. Also disclosed herein are methods of using an enzyme comprising DNA N-glycosylase activity to generate single-stranded circular nucleic acids.

Abstract: Interdigitated electrode arrays are very promising devices for multi-parameter (bio)sensing, for example the label-free detection of nucleic acid hybridisation for diagnostic applications. The current disclosure provides an innovative method for the affordable manufacturing of polymer-based arrays of interdigitated electrodes with ?m-dimensions. The method is based on a combination of an appropriate three-dimensional structure and a single and directional deposition of conductive material. The three-dimensional structure can be realized in a polymer material using a moulding step, for which the moulds are manufactured by electroplating as a reverse copy of a silicon master structure. In order to ensure sufficient electrical isolation and individual, but convenient, accessibility of the sensors in the array, the interdigitated electrode regions need to be complemented with specific features on the three-dimensional structure. Combined with the use of e.g.

Abstract: A method of diagnosing cancer by identifying differential modulation of each gene (relative to the expression of the same genes in a normal population) in a combination of genes selected from two groups of genes. Gene expression portfolios and kits for employing the method are further aspects of the invention.

Abstract: The invention concerns a nanostructured device (100) comprising a substrate (101), an intermediate layer (102), a zone (103) consisting of multiple three-dimensional structured sites (104) made of semiconductor material, having chemical species (106) fixed to the surface of said three-dimensional nanostructured sites (104). The inventive device is useful for making a biochip and an electronic memory.

Abstract: The present invention provides methods and compositions for the enrichment of target nucleic acids in a microarray system. In particular, the present invention provides methods and compositions for uniform enrichment of target nucleic acid molecules in a microarray format. The present invention also provides for intentionally non-uniform enrichment among target nucleic acid molecules.

Abstract: Arrays containing a transcriptome of a diseased tissue and methods of using the arrays for diagnosis, prognosis, screening, and identification of disease are provided herein. The transcriptome arrays from diseased tissue are useful for diagnosis of a disease by analysis of the genetic profile of a tissue sample specific to a disease state. The genetic profiles are then correlated with data on the effectiveness of specific therapeutic agents. Correlating expression profiles to the effectiveness of therapeutic agents provides a way to screen and select further patients predicted to respond to those therapeutic agents, thereby minimizing needless exposure to ineffective therapy.

Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.

Abstract: The present invention relates to a method for screening a gene involved in early recurrence of HCV-positive hepatocellular carcinoma associated with chronic hepatitis, comprising: determining an expression level of a gene in a noncancerous site from each of early and late recurrent cases of HCV-positive hepatocellular carcinoma associated with chronic hepatitis; and selecting a gene whose expression is increased in the early recurrent case compared with that in the late recurrent case. The present invention can provide a gene involved in recurrence of hepatocellular carcinoma.

Abstract: The present invention relates in general to the detection of antibiotic resistance determinants in Pseudomonas aeruginosa (P. aeruginosa). The present invention discloses a micro-array for the detection of antibiotic resistance determinants and mutations in said organism, a method for the detection of sad determinants and a kit. This micro-array concept offers the rapid sensitive and specific identification of antibiotic resistance profiles.

Abstract: The present invention provides compositions, including vectors, and methods for the rapid subcloning of nucleic acid sequences in vivo and in vitro. In particular, the invention provides vectors used to contain a gene of interest that comprise a sequence-specific recombinase target site. These vectors are used to rapidly transfer the gene or genes of interest into any vector that contains a sequence-specific recombinase target site located downstream of a regulatory element so that the gene of interest may be regulated.

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 new 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: The present invention relates to novel sequences for use in detection, diagnosis and treatment of cancers, especially lymphomas. The invention provides cancer-associated (CA) polynucleotide sequences whose expression is associated with cancer. The present invention provides CA polypeptides associated with cancer that are present on the cell surface and present novel therapeutic targets against cancer. The present invention further provides diagnostic compositions and methods for the detection of cancer. The present invention provides monoclonal and polyclonal antibodies specific for the CA polypeptides. The present invention also provides diagnostic tools and therapeutic compositions and methods for screening, prevention and treatment of cancer.

Abstract: The present invention provides an RNA interference induction element containing a nucleotide sequence selected from among the nucleotide sequences (a) to (c) below: (a) a nucleotide sequence containing SEQ ID NO:1 or a sequence complementary thereto; (b) a nucleotide sequence containing at least 15 continuous nucleotides present in the nucleotide sequence (a) above, and possessing RNA interference induction potential; (c) a nucleotide sequence having a homology of at least 70% to any one of the nucleotide sequences (a) and (b) above, and possessing RNA interference induction potential. Using the RNA interference induction element of the present invention, it is easily possible to knock down a desired target gene, and to produce a siRNA for a desired target gene.

Abstract: The present invention provides a method for combining the advantages of encoded molecule fragments made by split and mix synthesis with the advantages of template directed synthesis of molecules.

Abstract: The invention relates to methods of identifying inter-patient differences in genotype of PECAM-1 to diagnose and assess risk of arterial disease. It further relates to methods of identifying therapeutics agents for to treat coronary arterial disease, and to methods for determining and exploiting such differences to improve medical outcomes.

Abstract: The invention relates to nucleic acid molecules for use in detecting a target nucleic acid molecule which is a member of a class of nucleic acid molecules and which is characterised by a specific variant region, said nucleic acid molecule comprising (i) a nucleic acid stem region which comprises a nucleic acid interaction site directed to a conserved region of the class of which said target nucleic acid molecule is member, or part thereof and which conserved region is located proximally to a variant region; operate y linked to (ii) a nucleic acid recognition region comprising at least two nucleotides. The nucleic acids are used in arrays and are an efficient means of screening molecules exhibiting a unique nucleotide sequence within a randomly varying population. The invention is useful in monitoring the effectiveness of therapeutic drug therapies and the progression of medical conditions, characterised by the presence of clonal populations of cells, particularly clonal lymphocyte populations.

Abstract: A rapid, safe method for predicting sepsis, or a condition similar to sepsis, in a mammal is disclosed, which comprises the following steps: I) isolating RNA from a biological sample of a mammal; ii) labeling the isolated RNA of step I) with a detectable marker; iii) hybridizing the labeled isolated RNA of step ii) with at least one DNA of genes Seq.-ID 1 to Seq.-ID 6705 (Table 1), which is spotted onto a microarray and which is a sepsis-specific gene or gene fragment, under the reaction conditions for hybridizations; iv) quantitatively recording labeling signals of the hybridized RNA of step iii) in an expression profile; v) comparing the expression profile of step iv) with a control sample with respect to a stronger or weaker expression of genes or gene fragments which are specific for sepsis; and vi) combining the expression profile of step v) with protein- and metabolite patterns of the biological sample.

Abstract: The present invention relates to methods for identifying tissue sites in a chronic wound that are suitable for debridement and whether debridement procedure has been successful using particular biological markers of the cells within the tissue sites of the chronic wounds.

Abstract: A complex able to detect an analyte (CRA) comprising a particle expressing on its outer surface a compound having specific binding capability (CDCLS) for the analyte and stably including at least one nucleic acid reporter sequence being univocally associated to the CDCLS; process for its construction and uses thereof.

Abstract: The invention provides a method for generating a polynucleotide sequence or population of sequences from parent polynucleotide sequences, the method comprising the steps of (a) providing a first population of polynucleotide molecules and a second population of polynucleotide molecules, the first and second populations together constituting plus and minus strands of parent polynucleotide sequences, (b) digesting the first and second populations of polynucleotide molecules with a nuclease to generate polynucleotide fragments, (c) contacting said polynucleotide fragments generated from the plus strands with fragments generated from the minus strands and (d) amplifying the fragments that anneal to each other to generate at least one polynucleotide sequence encoding one or more protein motifs having an altered amino acid sequence as compared to those encoded by the parent polynucleotides, wherein the degree of sequence variability in a selected region of the at least one polynucleotide molecule produced in step (d

Abstract: A functionalized platform for a polymer array, comprising a substrate, and a metal oxide layer that attaches a functionalized alkyl phosphonate compound is described together with related array methods and systems.

Abstract: The present invention provides a method of selectively amplifying fetal DNA sequences from a mixed, fetal-maternal source. This method utilizes differential methylation to allow for the selective amplification of trophoblast/fetal specific sequences from DNA mixtures that contain a high proportion of non-trophoblast/fetal DNA. The invention also provides methods of using the amplified fetal DNA sequences for aneuploidy detection.

Abstract: This invention relates to a bioreaction execution system and bioreaction execution method capable of producing electric fields in a flow channel, into which a solution with a target gene contained therein is dropped, on a DNA chip and causing the target gene to electrophoretically migrate, the DNA chip, an information processing system and information processing method, a program, and a recording medium. An AC supply unit 41 supplies an AC current to an electromagnetic induction generator unit 42, the electromagnetic induction generator unit 42 generates electromagnetic induction based on the thus-supplied AC current, and generates a magnetic field in adjacent to a flow channel which is formed on a mounted DNA chip 43 and into which a solution with a target gene contained therein is dropped. One of electric fields produced to negate the thus-generated magnetic field is canceled, while the other electric field is maintained.

Abstract: A first embodiment is a breast cancer prognosticator comprising a detection mechanism consisting a 15-gene signature. In addition there are embodiments comprised of 23-gene signatures and 28-gene signatures. The 28-gene signature may also be used for the prognosis of ovarian cancer. A second embodiment is a method to determine metastatic potential, relapse potential, or both in breast cancer patients comprising collecting a sample from an individual, removing marker-derived polynucleotide from said sample, using a detection mechanism to search for positive matches of said polynucleotides and either the 15, 23, or 28-gene signatures, and developing a quantitative expression profile. Utilizing risk analysis the individual can be placed into one of two or more groups predicting risk and/or clincopathogic variables.

Abstract: Mitochondrial DNA deletions useful for the detection of cancers and sun exposure are provided. In particular, methods and kits for detecting mitochondrial DNA deletions for the early detection, diagnosis and progression of prostate cancer, sun exposure and non-melonoma skin cancer are provided.

Abstract: The present invention relates to a method of diagnosing a predisposition of a multiple sclerosis (MS) patient for responsiveness to a treatment of MS by administration of interferon-? (IFN-?) and/or interferon-? (IFN-?) and means to perform the method. Furthermore, the invention relates to a method of diagnosing a predisposition of a patient for developing multiple sclerosis (MS) and corresponding means.

Abstract: It is an object of the present invention to provide a method for identifying brewer's yeast genes associated with alcoholic beverage flavor, to allow production of alcoholic beverages with desirable flavor by controlling the expression of the identified genes. In order to achieve this object, there is provided a method for identifying brewer's yeast genes using gene analysis means employing a DNA array or a DNA array and two-dimensional electrophoresis, a DNA array binding identified genes, and a method of selecting brewer's yeast using the DNA array.

Abstract: The invention provides the identification of oncogenic pathways activated in cytologically normal airway cells of individuals having or at risk of having lung disease, as well as specific gene expression patterns (biomarkers) associated with pathway activation. These biomarkers and pathways may provide prognostic and/or diagnostic indicators in lung disease, e.g., lung cancer. Additionally, these pathways and biomarkers may provide therapeutic targets for the treatment of lung disease, as well as markers for the assessment of treatment efficacy.

Abstract: This invention relates to a series of PCR primers that will allow the simultaneous amplification of regions of the clinically significant ABO and RHD genes.

Abstract: The invention relates to the early detection of sepsis and the use of particular sets of biomarkers. Combinations of biomarkers representing changes in expression levels of specific genes are provided and, in particular, the use of microarrays to detect such changes of expression and to provide early diagnostic information is provided.

Abstract: An array-based method for performing genomic analysis is provided. In certain embodiments, the method may comprise: a) contacting a sample comprising genomic DNA with a Type IIB restriction enzyme to produce Type IIB fragments; b) directly labeling the Type IIB fragments with a fluorescent label to produce labeled fragments; c) contacting the labeled fragments with an array to produce a contacted array; and d) reading the contacted array to produce data. In certain instances, the data may be analyzed to determine the copy number of a genomic region in the sample. Also provided are arrays and kits useful to practice the method.

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 and are based on rational design informed by examination of publicly available databases of human antibody sequences.

Abstract: Walk-through mutagenesis and natural-variant combinatorial fibronectin Type III (FN3) polypeptide libraries are described, along with their method of construction and use. Also disclosed are a number of high binding affinity polypeptides selected by screening the libraries against a variety of selected antigens.