Abstract: The present invention provides a linker preferably used when constructing an mRNA/cDNA-puromycin-protein conjugate used in an in vitro virus method, and an mRNA/cDNA-puromycin-protein conjugate constructed using that linker. More specifically, the present invention provides a linker for ligating mRNA and puromycin or a puromycin-like compound to construct an mRNA/cDNA-puromycin-protein conjugate, the linker comprising a single-stranded RNA as a main backbone, and having, in this main backbone, a solid phase binding site for binding an mRNA-puromycin-protein conjugate to a solid phase site, and a pair of cleavage sites provided at locations surrounding the solid phase binding site; an mRNA-puromycin-protein conjugate constructed using this linker; an mRNA bead or an mRNA chip comprising this conjugate; a protein chip produced from this mRNA chip; and a diagnostic kit using the mRNA bead or the mRNA chip.

Abstract: The present invention provides polypeptides that contain one or more PDZ loop-variants and are useful in the detection of pathogens and disease-associated molecules. The polypeptides of the invention are also useful in the diagnosis, treatment, and prevention of diseases. Also provided are methods of preparing polypeptides of the invention.

Abstract: Methods for selecting a medication for a patient are described that include determining the patient's genotype for a panel of genes and selecting the medication based on the genotype. Articles of manufacture also are provided that include nucleic acid molecules for detecting alleles of genes encoding drug metabolizing enzymes and genes encoding products involved in neurotransmission.

Abstract: The present invention relates a method of generating modified binding moieties comprising a cytokine binding domain consisting of a first FmIII-like domain and a second FnIII-like domain in which at least one amino acid residue within the cytokine binding domain in modified such that the binding characteristics of the cytokine binding domain are altered, and/or, the solubility and/or stability of the binding moiety is improved.

Abstract: The invention provides genes that are unique either to Ehrlichia ruminantium strain Gardel or to Ehrlichia ruminantium strain Welgevonden, or allelic couples which are present in both strains but whose sequences differ between the two strains, as genetic markers to differentiate between these two strains. The invention also provides diagnostic methods using these genetic markers.

Abstract: The invention provides anti-apoptotic agents and therapies and uses thereof. Specifically, the anti-apoptotic agents and therapies involve human Xist gene, Xist RNA, Xist gene product, and antagonists and small molecule mimics of these nucleic acids and proteins.

Abstract: Nucleic acid molecules comprising a SNP site at position 1296 of bovine uterine milk protein (UTMP) coding sequence (SEQ ID NO: 1), which SNP indicates a desirable productive life in a dairy cattle. Also disclosed are an array or a kit comprising the same, a method for detecting the SNPs, a method for progeny testing of cattle, and a method for selectively breeding of cattle.

Abstract: About 70% to 80% of breast cancers express estrogen receptor-? (ER?), and estrogens play important roles in the development and growth of hormone-dependent tumors. Together with lymph node metastasis, tumor size and histological grade, ER status is considered one of the prognostic factors in breast cancer, and an indicator for hormonal treatment. 147 genes and 112 genes with significant P-value and having significant differential expression between ER+ and ER? tumors were identified from the LCM data set and bulk tissue data set, respectively. 61 genes were found to be common in both data sets, while 85 genes were unique to the LCM data set and 51 genes were present only in the bulk tumor data set. Pathway analysis with the 85 genes using Gene Ontology suggested that genes involved in endocytosis, ceramide generation, Ras/ERK/Ark cascade, and JAT-STAT pathway may play roles related to ER.

Abstract: The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted stem cell growth factor-like polypeptides. In particular, the invention relates to novel stem cell growth factor-like polypeptides, including novel proteins named SCGF3248Fk081_aa2, SCGF3248Fk081_aa1, SCGFFk081_aa3, and SCGF323401Fe131_aa1. Other aspects of the invention include vectors containing processes for producing novel human secreted stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides.

Abstract: A biosensor for use in detecting the presence of diseases, the biosensor comprising a detector for detecting a presence of at least one marker indicative of a specific disease. A method of determining efficacy of a pharmaceutical for treating a disease or staging disease by administering a pharmaceutical to a sample containing markers for a disease, detecting the amount of at least one marker of the disease in the sample, and analyzing the amount of the marker in the sample, whereby the amount of marker correlates to pharmaceutical efficacy or disease stage. Markers for gynecological disease selected from the list in Table 8. An immuno-imaging agent comprising labeled antibodies, whereby the labeled antibodies are isolated and reactive to proteins overexpressed in vivo. Informatics software for analyzing the arrays of claim 17, the software including analyzing means for analyzing the arrays.

Abstract: Provided is a novel endogenous antisense RNA expression analysis system capable of comprehensively and highly-precisely detecting endogenous antisense RNA including noncoding antisense RNA. A probe set containing one or more probes designed for an antisense strand sequence (Artificial Antisense Sequence: AFAS) under the conditions optimal for hybridization, by artificially defining an antisense strand of known cDNA; a microarray containing the AFAS probe set; detection method of endogenous antisense RNA wherein the microarray and RNA labeling by random priming are combined, and the like.

Abstract: Methods, reagents and kits are provided for the production and use in detection assays of labeled nucleic acid molecules wherein a labeling molecule is attached directly to the 3? end of the nucleic acid molecules.

Abstract: The present invention is directed to novel methods of treating, identifying or diagnosing a hyperproliferative disorder in a patient in need thereof. The methods of the invention include administering to a patient a composition comprising a binding molecule which binds to a cell surface expressed glycoprotein expressed predominantly in tumor or tumor-associated cells. In particular, the therapeutic and diagnostic methods of the present invention include the use of a binding molecule, for example an antibody or immunospecific fragment thereof, which specifically binds to a membrane associated molecule, variant polypeptide or fragment thereof. The present invention is based, at least in part, on the discovery of membrane associated proteins, i.e., nucleic acid molecules which encode membrane proteins and the use of these molecules to generate custom arrays to screen for markers associated with various diseases and disorders, e.g., cancer, e.g.

Abstract: The invention provides novel oligonucleotides and methods of using the same for detection or measurement of specific nucleic acid molecules. The invention also features nucleic acid arrays comprising the oligonucleotides of the invention. An oligonucleotide of the invention comprises (1) a reporter-binding sequence capable of hybridizing to a fluorrophore-labeled reporter sequence and (2) a hairpin-forming sequence capable of forming a stem-loop. Formation of the stem-loop modifies (e.g., quenching) the fluorescence signals of the reporter sequence when the reporter sequence is hybridized to the oligonucleotide. This can be achieved, for example, by bringing one or more guanine based in the oligonucleotide into close proximity to the fluorophore(s) of the reporter sequence by virtue of the formation of the stem-loop. Disruption of the stem-loop, such as by hybridization of a target sequence to at least part of the hairpin-forming sequence, produces a detectable change in the fluorescence signals.

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 PTP1B.

Abstract: A method of: providing a solid surface having a dendrimer molecule bound thereto and a single-stranded probe nucleic acid immobilized to the dendrimer; contacting the solid surface with a sample suspected or known to contain a double-stranded complimentary target nucleic acid; denaturing the target nucleic acids at thermal conditions and in a salt concentration sufficient to denature the target nucleic acids to produce denatured nucleic acids; and cooling the sample to allow hybridization of the denatured nucleic acids to the probe nucleic acids. An article having: one or more paramagnetic microbeads; a dendrimer molecule bound to the beads; and a probe nucleic acid immobilized to the dendrimer.

Abstract: Provided are microarrays comprising spots comprising mixtures of cDNA molecules, the cDNA mixture being complementary and substantially quantitatively proportional to a mixture of mRNA molecules present in a cell or group of cells. Also provided are methods for determining expression of a gene in a cell or group of cells using the invention microarrays. Additionally provided are methods of determining the difference in expression of a first gene between a first cell or group of cells and a second cell or group of cells, using the invention microarrays. Also provided are microarrays comprising short RNAs, and methods of using these microarrays for detecting and quantifying microarrays in cells.

Abstract: The present invention provides methods and compositions for predicting patient responses to cancer treatment using a proliferation gene signature. 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: The invention relates to oligonucleotides, which are suited as primers for amplifying DNA of genital human papilloma viruses (HPV), to oligonucleotides, which are suited for use as probes for typifying genital HPV genotypes, to methods for amplifying the DNA of genital human papilloma viruses (HPV), to methods for detecting and/or identifying genital HPV genotypes, to nucleotide microarrays containing the oligonucleotides, to kits and to the use of the oligonucleotides for amplifying or typifying genital HPV genotypes, for the diagnosis and/or early diagnosis of diseases and for producing agents for diagnosing diseases.

Abstract: A separation method of single-stranded nucleic acid characterized in that nucleic acid amplification is performed using a first primer to which a second substance capable of binding specifically to a first substance is bound and a second primer to which the second substance is not bound, and double-stranded nucleic acid obtained by the nucleic acid amplification is bound to the first substance, and the double-stranded nucleic acid bound to the first substance is dissociated into a single strand, and a separation apparatus of single-stranded nucleic acid characterized by having a nucleic acid amplification part 1 for performing nucleic acid amplification using a first primer to which a second substance capable of binding specifically to a first substance is bound and a second primer to which the second substance is not bound, a binding part 2 for binding double-stranded nucleic acid obtained by the nucleic acid amplification to the first substance, and a dissociation part 3 for dissociating the double-stranded

Abstract: Identified herein are different forms of sweet and umami receptor encoding sequences that occur in different human populations. In particular, there are provided several single nucleotide polymorphisms (SNPs) that occur within the exons/coding sequence (and are therefore coding SNPs, cSNPs) of one of the three T1R genes. Some SNPs cause amino acid substitutions, while others introduce a chain termination codon, rendering a truncated product. Differences in these genes are believed to affect the sense of taste of individuals, such that individuals with different SNPs (or different haplotypes) are believed to perceive the taste of sweet or umami (e.g., glutamate) 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 groups and populations who perceive tastes differently. This in turn allows the taste preferences of these groups to be addressed at the molecular level.

Abstract: Aspects of the invention relate to the design and synthesis of nucleic acid libraries containing non-random mutations or variants. Aspects of the invention provide methods for assembling libraries containing high densities of predetermined variant sequences. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express a predetermined polypeptide from a library of nucleic acids having silent sequence variants. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express predetermined RNA variants that encode the same polypeptide sequence.

Abstract: The present invention concerns a protein mixture comprising at least a first fusion protein comprising a protein or protein fragment, and an interaction domain and a protein translocation sequence, which effects that the fusion protein upon expression in a bacterium is translocated through the cytoplasmic membrane in an essentially unfolded state and at least a second fusion protein comprising a protein or protein fragment, and an interaction domain and a protein translocation sequence which effects that the fusion protein is translocated through the cytoplasmic membrane upon expression in a bacterium in an essentially folded state, wherein the interaction domain of the first protein can bind to those of the second protein.

Abstract: The invention provides methods and devices for high throughput single molecule sequencing of a plurality of target nucleic acids using a universal primer. Devices of the invention comprise a plurality of oligonucleotides, each having the same sequence, bound to a solid support, and ligated to a plurality of target nucleic acids.

Abstract: Provided is a method for noncovalently immobilizing a biomolecule on a solid substrate, including: providing a solid substrate having a first functional group attached thereto, the first functional group having a hydrogen bond donating ability; and reacting a mixture of a compound having a hydrogen bond accepting ability and a biomolecule functionalized with a second functional group, with the surface of the substrate, the second functional group having a hydrogen bond donating ability, in order to noncovalently immobilize the biomolecule on the substrate.

Abstract: The present invention relates to the detection of antibiotic resistance determinants in Staphylococcus aureus. The present invention discloses a micro-array for the detection of antibiotic resistance determinants and mutations in Staphylococcus aureus, a method for the detection of the determinants and mutations, and a kit.

Abstract: The present invention to a panel comprising at least two pairs of primers that are complementary to at least two different reporter genes, the expression of which are i) either up- or down-regulated upon cell differentiation, and ii) display a similar expression profile in at least two different cell lines of the same kind of cells. The cells may be blastocyst-derived stem (BS) cells or human blastocyst-derived stem (hBS) cells. Furthermore, the present invention relates to the use of a calculated expression index for quantifying and evaluating the expression of the reporter genes, which for example can be used for assessing the state of differentiation of a cell population, such as, e.g. a hBS cell population.

Abstract: The present invention provides methods, systems and equipment for the prognosis, diagnosis and selection of treatment of AML or other types of leukemia. Genes prognostic of clinical outcome of leukemia patients can be identified according to the present invention. Leukemia disease genes can also be identified according to the present invention. These genes are differentially expressed in PBMCs of AML patients relative to disease-free humans. These genes can be used for the diagnosis or monitoring the development, progression or treatment of AML.

Abstract: mRNA transcript profiling can be used to formulate molecular predictors of distant metastasis for primary NPCs. The predicted results are highly correlated with short metastasis-free and overall survival. Predictions are made using 52-genes based and 12-genes based predictors.

Abstract: Gene-Based Algorithmic Cancer Prognosis relates to methods and systems for prognosis determination in tumor samples. The methods and systems measure gene expression in a tumor sample and applying a gene-expression grade index (GGI) or a relapse score (RS) to yield a number c risk score.

Abstract: The present invention provides methods and kits for predicting transplant rejection or tolerance. Methods for predicting the probability of cardiac allograft rejection via profiling of peripheral blood gene expression are also provided.

Abstract: In general, the invention provides methods and compositions for the in vitro production of ribonucleoprotein complexes and related multimolecular complexes useful for cell-free methods of protein production.

Abstract: Nucleic acid arrays and methods of using nucleic acid arrays are disclosed.

Abstract: The invention provides articles of manufacture which are arrays, reagents, kits, and methods for diagnosis and/or prognosis of diseases with genomic aberrations. The methods of the invention identify differences between DNA samples from normal and disease tissues that are ascertained using comparative genomic hybridization (CGH) with microarrays of genomic fragments covering the whole genome of an organism, or microarrays containing subsets of the genome that are identified by the methods herein, for example, the long arm of chromosome 2 associated with prostate cancer. The detected genomic aberrations, are correlated to specific clinical outcomes, such that specific patterns of genomic aberration—disease association are identified in the majority of samples. The invention also provides genomic DNA arrays encompassing regions, the aberration of which was correlated to specific disease outcomes, for diagnosis/prognosis of such diseases.

Abstract: A method for determining the prognosis of a CD5+DLBCL patient and a CD5-DLBCL patient is provided. It is determined that, in the chromosomal DNA from a patient with lymphoma, (1) the prognosis of the CD5+DLBCL patient with amplification of 13q21.1-q31.3 region is poor; (2) the prognosis of the CD5+DLBCL patient with deletion of 1p36.21-p36.13 region is poor; and (3) the prognosis of the CD5-DLBCL patient with amplification of 5p15.33-p14.2 region is good.

Abstract: The present application pertains to products and methods related to the ability of short nucleotide oligomers to bind the tertiary or globular structure of nucleic acids. This application discloses libraries of short oligomers and methods for using these libraries.

Abstract: Reagents which regulate human RC Kinase activity and reagents which bind to human RC Kinase gene products can be used to regulate this protein for therapeutic effects. Such regulation is particularly useful for treating chronic obstructive pulmonary disease, asthma, cancer, and diseases in which cell signaling is defective.

Abstract: The methods and compositions of the invention find use in the clinical diagnosis of cholestasis related syndromes, particularly PFIC types 1, 2, and 3; BRIC types 1 and 2; Alagille syndrome, and alpha 1-antitrypsin deficiency. The compositions of the invention include isolated nucleic acid molecules and oligonucleotide pairs suitable for use in amplifying regions of cholestasis related genes. Compositions of the invention include a cholestasis related gene resequencing microarray suitable for determining the nucleotide sequence of a region of a cholestasis related gene. Knowledge of the nucleotide sequence of one or more regions of a patient's cholestasis related gene allows diagnosis of the patient's syndrome.

Abstract: Proteins including engineered sequences which inhibit proteases are disclosed, including proteins having two or more engineered Kunitz domains, and uses of such proteins.

Abstract: The invention is based on the discovery that the human protein referred to herein as INSP181 protein is a lipocalin.

Abstract: Methods for predicting an individual's genetic risk for developing ARMD is disclosed, as are arrays and kits which can be used to practice the method. The method includes screening for mutations and/or polymorphisms in ARMD-associated molecules, such as CFH, LOC387715, BF, C2, ABCR, Fibulin 5, VMD2, TLR4, CX3CR1, CST3, MnSOD, MEHE, paraoxonase, APOE, ELOVL4 and hemicentin-1.

Abstract: The present invention includes a method and composition of storing and preserving biofilms for input and output of high-density information. One form of the present invention is a fabricated biofilm storage device with a biologic material applied to a substrate to form, e.g., a dry thin film stable at room temperature for extended periods of time. Another form of the present invention is a method of fabricating a biofilm storage device in which a biologic material is applied to a substrate under conditions that promote alignment of the biologic material on the substrate. The composition, method, and kit of the present invention have universal application in biologics, magnetics, optics and microelectronics.

Abstract: The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human stem cell growth factor-like protein. These polynucleotides comprise nucleic acid sequences isolated from cDNA libraries from human testis cells (Hyseq clone identification numbers 2880984 and 2881695), from human fetal skin (Hyseq clone identification number 15375176), adult spleen (Hyseq clone identification number 14856094), and human endothelial cells (Hyseq clone identification numbers 13804756, 13687487, 13804756). Other aspects of the invention include vectors containing processes for producing novel human stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides.

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 procedure for linking cognate pairs of VH and VL encoding sequences from a population of 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, in particular polymerase chain reaction (multiplex PCR). The method is particularly advantageous for the generation of cognate pair libraries as well as combinatorial libraries of variable region encoding sequences from immunoglobulins. The invention also relates to methods for generation of chimeric human/non-human antibodies and expression libraries generated by such methods.

Abstract: A biosurface structure array (BSSA) comprising a plurality of tester areas whereby each area has a surface topology whose features are defined on a micro- or nanometer scale. The BBSA of the invention may further comprise adsorbed compounds to one or more of the tester fields, e.g. active biological compounds or polymers.

Abstract: Methods and compositions related to novel genes associated with type 2 diabetes mellitus.

Abstract: Rodent gene expression data, in particular, gene expression profiles, are created and used to predict the efficacy of therapeutic agents on human biological conditions. Gene Profile data sets are derived from rodent subject samples and include quantitative, substantially repeatable measures of a distinct amount of RNA or protein constituent(s) in a signature panel selected such that measurement of the constituent(s) enables measurement of a biological condition of interest in both human and rodent subjects. Such profile data sets may be used to predict the therapeutic efficacy of a therapeutic agent in humans.

Abstract: A method of producing a DNA array for analyzing a DNA modification (for example, methylation), comprising (1) preparing a mixture of DNA fragments in which a modified base (for example, methylated cytosine) or a base (for example, cytosine) is exposed, (2) bringing the mixture of DNA fragments into contact with an antibody specific to the modified base (for example, methylated cytosine) or the base (for example, cytosine), and separating the mixture into a group consisting of DNA fragments which form an immunocomplex and another group consisting of DNA fragments which do not react with the antibody, or a group consisting of DNA fragments showing a high affinity for the antibody and another group consisting of DNA fragments showing a low affinity for the antibody, (3) identifying all or part of DNA fragments contained in each of the DNA fragment groups, and (4) arranging one or more nucleic acids capable of hybridizing with any one of the identified DNA fragments on a substrate, is disclosed.

Abstract: This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.