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

Abstract: Improved systems and methods for reducing costs and increasing yields of cellulosic ethanol including compositions of matter comprising plant biomass and cell wall-modifying enzyme polypeptides and transgenic plants expression cell wall-modifying enzyme polypeptides.

Abstract: In labeling a cell, and separating and collecting the cell according to a degree of the labeling using a cell separator, effects on the cell is minimized and the use of the collected cell is facilitated, thereby, when labeling a cell, the cell is labeled in the state where interaction of each cell is retained. In the labeling, a specific labeling material present on a surface of a target cell is taken in the cell via a transporter, and the cell is dispersed one by one to separate the same with a cell separator. Immediately after the separation, the cell is put in a solution not containing the specific labeling substance to remove the specific labeling substance taken in the cell. This series of steps is continuously conducted with a cell separation chip.

Abstract: The invention provides reliable, reusable materials, system and methods for use in nucleic acid binding assays between a nucleic-acid binding assay molecule and a robust unimolecular target. In a preferred embodiment, the target is a nucleic acid-containing molecule, L1-X1-L2-X2 (where L1 is the linker to the solid support, and L2 is the linker between the two nucleotide-pairing regions, X1 and X2; L2 folds such that double-stranded DNA structure forms between X1 and X2). L2 is a polynucleotide three nucleotides in length, having the sequence GNA, where N is A, G, C, T, or U. A typical assay uses a target array, where multiple targets are bound to a solid surface. The linker, L1, of the nucleic acid target to the supporting surface is useful although it is significantly longer than suggested in the art. The length of L1 is preferably 8 to 30 nucleotides in length, more preferably from 10 to 20 nucleotides.

Abstract: The present invention relates to a method for synthesising templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The intion allows the generation of libraries which can be screened for e.g. therapeutic activity.

Abstract: In labeling a cell, and separating and collecting the cell according to a degree of the labeling using a cell separator, effects on the cell is minimized and the use of the collected cell is facilitated, thereby, when labeling a cell, the cell is labeled in the state where interaction of each cell is retained. In the labeling, a specific labeling material present on a surface of a target cell is taken in the cell via a transporter, and the cell is dispersed one by one to separate the same with a cell separator. Immediately after the separation, the cell is put in a solution not containing the specific labeling substance to remove the specific labeling substance taken in the cell. This series of steps is continuously conducted with a cell separation chip.

Abstract: The present invention provides methods for the assessment of risk of developing acute coronary syndrome (ACS), arterial inflammation, or ACS-associated impaired vascular function, in smokers and non-smokers using analysis of genetic polymorphisms. The present invention also relates to the use of genetic polymorphisms in assessing a subject's risk of developing ACS, arterial inflammation, or ACS-associated impaired vascular function. Nucleotide probes and primers, kits, and microarrays suitable for such assessment are also provided.

Abstract: The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. Polypeptides, including enzymes and antibodies, and nucleic acids of the invention can be used in industrial, experimental, food and feed processing, nutritional and pharmaceutical applications, e.g., for food and feed supplements, colorants, neutraceuticals, cosmetic and pharmaceutical needs.

Abstract: This invention relates to DNA libraries based on plasmid or viral vectors that can express double-stranded RNA of 10-30 base pairs in length with all possible sequences, where each of the double stranded RNA is formed by a single RNA molecule in the form of hairpin, or formed by two separate RNA molecules with different 3?-overhangs. Each single member in such a DNA library encodes all components of a double stranded RNA as specified above. Such a library can be used in screening for double stranded RNA species that can induce a given phenotype without prior knowledge of their target genes. This invention further relates to a method to generate such a DNA library.

Abstract: The present invention provides for oligonucleotide arrays wherein the oligonucleotides comprise six-membered sugar-ring nucleosides, especially tetrahydropyran nucleosides, more specifically altritol nucleosides. The present invention also provides for the use of said oligonucleotide arrays for detecting target molecules in samples (diagnostic or experimental use). The present invention also provides for a method of detecting target molecules in samples by using said oligonucleotide arrays comprising six-membered sugar-ring nucleosides.

Abstract: The present invention provides combinatorial encoding nucleic acid tiling arrays and methods for their use and synthesis.

Abstract: The invention concerns constructs and libraries comprising antibody surrogate light chain sequences. In particular, the invention concerns constructs comprising VpreB sequences, optionally partnered with another polypeptide, such as, for example, antibody heavy chain variable domain sequences, and libraries containing the same.

Abstract: The present invention provides substrates having a plurality of micro-locations on its surface. Each micro-location has an effective dose of an ion beam treatment such that the plurality of the micro-locations exhibit an affinity to a compound that is different from the affinity of the remainder of the substrate surface to that compound. The substrates of the invention can be utilized to form microarrays of biological molecules, such as oligonucleotides or peptides. Such microarrays can find a variety of applications. For example, they can be employed in large scale hybridization assays in many genetic applications, such as mapping of genomes, monitoring of gene expression, DNA sequencing, genetic diagnosis, and genotyping of organisms.

Abstract: The present invention relates to the use of gene activity markers for classification of patients suffering from infectious and non-infectious multiple organ failure, respectively. The present invention in particular relates to gene activity markers for classification of patients as “not infected without multiple organ failure” or as “not suffering from infectious multiple organ failure” or as “suffering from infectious multiple organ failure”, the gene activity markers being polynucleotides selected from the group consisting of: SEQ ID 1.1, SEQ ID 1.2, SEQ ID 1.3, SEQ ID 1.4, SEQ ID 1.5, SEQ ID 1.6, SEQ ID 1.7, SEQ ID 1.8 and SEQ ID 1.9 or partial sequences thereof.

Abstract: The invention is directed to isolated genomic polynucleotide fragments that encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA directed 50kD regulatory subunit (POLD2), vectors and hosts containing these fragments and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain SNARE YKT6, human glucokinase, AEBP1 protein and POLD2 and to diagnose, treat, prevent and/or ameliorate a pathological disorder.

Abstract: An apparatus that accelerates the determination of NN free energy of binding estimates for a large number of DNA oligomers using reconfigurable hardware and applies it to the design of high quality DNA code word libraries. The invention provides a reconfigurable hardware accelerator and method for implementing a nearest-neighbor based free energy calculation. The invention further provides a method to produce the maximum weight of the 2-stem common subsequence of two DNA oligonucleotides. In practice, the present invention comprises a general purpose microprocessor or computer, a hardware accelerator, and a software program.

Abstract: The present invention provides methods for the assessment, diagnosis, or prognosis of asthma exacerbation, by assessing the level of expression of asthma exacerbation gene products in a sample derived from a patient. The markers of the present invention can be used in methods to identify or evaluate agents capable of modulating marker expression levels in subjects with asthma.

Abstract: Substrates having nucleic acid polymers attached at varying surface densities and methods for creating substrates having nucleic acid polymers attached at varying surface densities are provided. Methods according to embodiments of the invention are adapted to the rapid synthesis of arrays of DNA polymers on a substrate surface. In embodiments of the invention an array of DNA molecules on a substrate comprises a plurality of DNA polymers attached to a trifunctional linker such that at least two DNA polymers are attached to one trifunctional linker that is attached to the surface of the substrate. By coupling trifunctional linkers to trifunctional linkers that are attached to a substrate surface, the density of DNA polymers on a substrate surface is increased.

Abstract: The present invention is directed to genetic sequence variations that can be used to predict whether a person will develop asthma. Disease is likely to occur if certain polymorphic forms the CCL11 gene, the CCL2 gene and the TLR7 gene are present.

Abstract: The invention is directed to isolated genomic polynucleotide fragments that encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA directed 50 kD regulatory subunit (POLD2), vectors and hosts containing these fragments and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain SNARE YKT6, human glucokinase, AEBP1 protein and POLD2 and to diagnose, treat, prevent and/or ameliorate a pathological disorder.

Abstract: The invention provides methods of detecting a nucleic acid. The methods comprise contacting the nucleic acid with one or more types of particles having oligonucleotides attached thereto. In one embodiment of the method, the oligonucleotides are attached to nanoparticles and have sequences complementary to portions of the sequence of the nucleic acid. A detectable change (preferably a color change) is brought about as a result of the hybridization of the oligonucleotides on the nanoparticles to the nucleic acid. The invention also provides compositions and kits comprising particles. The invention further provides methods of synthesizing unique nanoparticle-oligonucleotide conjugates, the conjugates produced by the methods, and methods of using the conjugates. In addition, the invention provides nanomaterials and nanostructures comprising nanoparticles and methods of nanofabrication utilizing nanoparticles. Finally, the invention provides a method of separating a selected nucleic acid from other nucleic acids.

Abstract: The invention is directed to methods for using sequence by ligation to sequence DNA immobilized on miniaturized, high density bead-based arrays. Methods are provided to fabricate an array of beads where the beads are coupled directly to a solid support. Methods are also provided to improve signal and reduce background in ligation-mediated DNA sequencing. In addition, methods are provided to improve the accuracy of reported tag counts when performing DNA sequencing by fluorescent nonamer ligation.

Abstract: Methods and compositions directed to improved universal antibody libraries that rationally exploit human diversity information contained within reference antibody libraries, such as universal antibody libraries, are disclosed. The disclosed processes involve use of a query CDR sequence to guide incorporation of human antibody diversity present within the reference library into cohort libraries of the invention. Methods for making and screening such cohort libraries for isolating therapeutics suitable for treating disease are also disclosed.

Abstract: A method of genetically screening large numbers of individuals to identify those individuals requiring follow-up testing for active Type I diabetes (T1D) is provided. The method includes obtaining a nucleic-acid containing biological sample from each individual and testing for the presence of specific combinations of HLA II alleles in the sample.

Abstract: The present invention relates to a novel combination of avian cell markers which make it possible to characterize the said cells according to their phenotype, whether they are StX cells, stem cells or germ cells. The present invention also relates to a method for characterizing avian cells with the said markers, and to a method for culturing avian cells, in which the cells are characterized by the method according to the invention.

Abstract: The present invention relates to a peptide nucleic acid (PNA) conjugated with multi-amine linkers, and a method to prepare the same and utilization thereof. More specifically, the method is characterized by conjugating monomers having multi-amine functionality sequentially at a PNA terminal, and effectively immobilizing the PNA conjugated with multi-amine linkers on a solid surface. A PNA array prepared using the PNA conjugated with multi-amine linkers exhibits improved sensitivity and specificity of signals for detecting target nucleic acids as compared to a PNA array using PNA probes having only one amine group. The PNA conjugated with multi-amine linkers can be utilized in nucleic acid detecting devices or kits for gene diagnosis such as PNA microarrays, PNA chips, PNA field-effect transistors and impedance detectors.

Abstract: The invention is directed to an isolated polypeptide which (a) is obtainable from a teleost; (b) has antimicrobial activity; (c) binds to oligoguanosine and/or CpG (SEQ ID NO:7); (d) comprises 58 strongly basic amino acids selected from the group consisting of K and R; (e) comprises 50 hydrophobic amino acids selected from the group consisting of A, I, L, F, W and V; (f) comprises 50 polar amino acids selected from the group consisting of N, C, Q, S, T and Y and (g) contains 11 lysine-rich motifs and antimicrobial fragments thereof as well as methods for preparing said polypeptides, compositions and libraries comprising said polypeptide(s) and uses of said polypeptide(s), particularly in treating microbial infections. The invention is further directed to a nucleic acid(s) encoding said polypeptide, microarrays comprising said nucleic acid(s) and uses for said nucleic acid(s).

Abstract: Controlling humidity at the surface of a solution containing analyte and ligand, e.g., for an assay, is disclosed, wherein the control of the humidity induces evaporative stirring in the solution to bring analyte and ligand into contact more quickly than when using diffusion. An oven which blows air in a controlled stream across slides, with wells containing reagent and analyte, is disclosed. Also disclosed is optical tape which can replace a conventional glass coverslip used for viewing of the reaction results.

Abstract: Polynucleotide sequences are provided that correspond to genes that are differentially expressed in atherosclerotic disease conditions. Methods for using these sequences to detect gene expression and/or for transcriptional profiling in mammals are also provided. The polynucleotide sequences of the invention may be used, for example, to diagnose atherosclerotic disease, to monitor extent of progression or efficacy of treatment or to assess prognosis of atherosclerotic disease, and/or to identify compounds effective to treat an atherosclerotic disease condition.

Abstract: The present invention provides methods for generating genetic profiles or analyses. Included are methods for conducting comprehensive, dynamic genetic analysis. Also provided are methods for determining genetic health scores for specific phenotypes, such as diseases, disorders, traits, and conditions, as well as for organ systems, for certain medical specialties, and for overall health.

Abstract: The present invention relates to products which are of nature B2+ A?, isolated from E. coli, and to their biological applications, in particular their medical (therapeutic, vaccine and diagnostic) and biotechnological applications. In the present application, the expression “of nature B2+ A?” is intended to mean presence at a frequency greater than 10% among the E. coli strains of group B2 of the ECOR collection, and at a frequency of less than 10% among the strains of group A of the same collection. A phylogenic determination method which makes it possible to rapidly and easily distinguish the groups A, B1, B2 and D of the E. coli species with more than 99% precision is in particular described.

Abstract: Novel proteins are provided herein, including proteins capable of catalyzing the acetylation of glyphosate and other structurally related proteins. Also provided are novel polynucleotides capable of encoding these proteins, compositions that include one or more of these novel proteins and/or polynucleotides, recombinant cells and transgenic plants comprising these novel compounds, diversification methods involving the novel compounds, and methods of using the compounds. Some of the novel methods and compounds provided herein can be used to render an organism, such as a plant, resistant to glyphosate.

Abstract: This invention provides for nonfluorescent, nonenzymatic, chemiluminescent aqueous assays in which the binding of two ligands is determined by a water soluble label system that emits light upon contact with a chemical energy transferring composition.

Abstract: The present invention provides methods of re-engineering or re-shaping an antibody from a first species, wherein the re-engineered or re-shaped antibody does not elicit undesired immune response in a second species, and the re-engineered or re-shaped antibody retains substantially the same antigen binding-ability of the antibody from the first species. In accordance with the present invention, a combinatorial library comprising the CDRs of the antibody from the first species fused in frame with framework regions derived from a second species can be constructed and screened for the desired modified antibody. In particular, the present invention provides methods utilizing low homology acceptor antibody frameworks for efficiently humanizing an antibody or a fragment thereof. The present invention also provides antibodies produced by the methods of the invention.

Abstract: The present invention relates to methods and devices for amplifying nucleic acid, and, in particular, amplifying so as to generate products on a surface without the use of emulsions. In a preferred embodiment, a plurality of groups of amplified product are generated on the surface, each group positioned in different (typically predetermined) locations on said surface so as to create an array.

Abstract: The invention provides a microcapsule array comprising a plurality of microcapsules immobilised on a surface, optionally in microwells in said surface. Each of the microcapsules comprises an outer layer or shell defining a microcapsule interior, said outer layer having a permeability towards a nanoscale species which is dependent on an environmental condition to which said array is exposed.

Abstract: Disclosed is a method for identification of microbial pathogens in a body fluid sample comprising the following steps: a) providing a body fluid sample; b) lysing the microbial pathogens and performing a nucleic acid amplification reaction on the microbial DNA encoding 16S or 18S rRNA wherein or whereafter the amplified nucleic acids are labelled; c) contacting the labelled amplified nucleic acids of step b) with a microarray comprising on defined areas on the microarray's surface immobilised probes for microbial DNA encoding 16S or 18S rRNA from microbial pathogens; d) detecting the binding of one or more species of the labelled amplified nucleic acids to a probe by detecting a labelled amplified nucleic acid being specifically bound to the microarray; and e) identifying a microbial pathogen in the body fluid sample by correlating the detected binding of the labelled amplified nucleic acids with the defined areas of the immobilised probes for microbial DNA encoding 16S or 18S rRNA from microbial pathogens.

Abstract: The present invention relates to oligonucleotides for detection of sepsis-causing bacteria and a detection method using the oligonucleotides, more particularly to a microarry comprising at least one of gram positive bacteria-specific and gram negative bacteria-specific oligonucleotides, sepsis-causing bacteria's genus-specific and species-specific oligonucleotides designed from the ITS target region which is hypervariable base sequence of sepsis-causing bacteria as probes, and a detection method and a diagnosis kit by using the same. According to the present invention, the present invention can provide an antibiotics therapy for accurately removing infectious agent related to sepsis by detecting existence of sepsis-causing bacteria and identifying gram positive- and gram negative-bacteria and genus and species of the bacteria, at once. And, the present invention can prevent a patient from abuse and misuse of antibiotics and decrease time of hospital treatment and medical cost of the patient.

Abstract: A process is provided for identifying a complementary target nucleic acid. The process includes the hybridization of a nucleic acid probe to a carrier to form a nucleic acid probe-carrier complex. The complex is placed in a compartment bounded by a media permeable to the nucleic acid probe and exclusive of both the carrier and the complex. The complex is then denatured, with the nucleic acid probe transported through the media and into contact with the target nucleic acid. The nucleic acid probe hybridizes to the complementary target nucleic acid to yield a probe-target double stranded complex. A non-complementary nucleic acid probe, independent probe-target complex is returned to the compartment and given an opportunity to rehybridize to the carrier. A determination as to whether at least one of the complementary target nucleic acid or the carrier is present as a complex provides information as to probe sequences complementary to the target nucleic acid.

Abstract: An expression library comprising a repertoire of nucleic acid sequences each encoding at least part of a variable domain of a heavy chain derived from an immunoglobulin naturally devoid of light chains and its use in producing antibodies, particularly fragments thereof, is disclosed. The invention provides a method for preparing antibodies, or fragments thereof, having a specificity for a target antigen which avoids the need for the donor previously to have been immunised with the target antigen.

Abstract: The invention is directed to enzyme variants, responsiveness thereof to cofactors, and in vivo assays for testing the activity of enzyme variants as well as the responsiveness thereof to cofactors.

Abstract: Provided are methods, kits and arrays for use in determining whether a scar of interest is keloid or non-keloid in nature. These determine keloid or non-keloid nature based on comparison of gene expression in the scar of interest with expression in a control sample. If expression of at least one gene, selected from the group of genes set out in Table 1, is increased in a sample representative of gene expression in the scar of interest compared to expression of the same gene (or genes) in the control sample this indicates that the scar of interest comprises a keloid.

Abstract: The present invention provides compositions and methods for binding and/or modulating enzymatic activity of human protein tyrosine phosphatases such as PTP1B. Additionally, the invention provides methods of identifying and using such nucleic acid ligands.

Abstract: A method of selecting a set of normalization probes for use on a comparative genome hybridization array is provided. In certain embodiments, the method includes: a) selecting a first region of a genome to be evaluated by comparative genome hybridization to produce data; b) selecting a second region of the genome for normalization of the data, and c) selecting from a set of candidate probes a sub-set of normalization probes that detect the second region.

Abstract: The present invention relates to the field of medicine and biology. It concerns a novel test for screening and for therapeutic follow-up in oncology. More particularly, it relates to diagnostic and/or therapeutic tests in oncology and on neurodegenerative diseases. It is a diagnostic test and a prognostic test for various cancers (breast cancer, bladder cancer, ovarian cancer, lung cancer, skin cancer, prostate cancer, colon cancer, liver cancer, gliboblastoma, sarcoma, leukemia, etc.) and therapeutics solutions for specific neurodegenerative diseases. More particularly, the invention concerns the use of the LIV21 protein, LIV21 gene and of derivatives thereof as diagnostic and prognostic markers for cancers. The invention therefore concerns the detection of the LIV21 protein with a kit comprising LIV21-specific antibodies.

Abstract: The invention relates to the use of gene expression profiles for predicting the probability of recurrence or metastases to develop in remote organs of patients from which a primary colon carcinoma has been removed.

Abstract: This invention relates to a composition, kit, or DNA chip comprising polynucleotides and antibodies as probes for detecting, determining, or predicting the presence or metastasis of esophageal cancer, and to a method for detecting, determining, or predicting the presence or metastasis of esophageal cancer using the same.

Abstract: The present Invention provides novel methods for immortalizing cells that secrete antibodies of one or more specific isotypes. Polyclonal, oligoclonal, and monoclonal populations of cells obtained using the methods of the Invention can be screened on the basis of the functional and/or binding activities of the antibodies they secrete, for example directed to antigens of human or viral origin having medical interest, in cell culture conditions. Using these methods, human B cells that secrete antibodies binding human Cytomegalovirus, Herpes Simplex Virus, or HSP60 protein have been efficiently immortalized with Epstein-Barr virus.

Abstract: Devices formed as optically readable substrates are provided having a high feature density (e.g., attachment or deposition sites) in arrays comprising macromolecules, specifically amplicons, and devices and methods are provided for analysis of target nucleic acids having an undetermined sequence.

Abstract: This invention provides compositions and methods for genetic testing of an organism and for correlating the results of the genetic testing with a unique marker that unambiguously identifies the organism. The markers may be internal markers, such as for example single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), or other sites within a genomic locus. Alternatively, the markers may be external, such that they are separately added to the genetic sample before testing.