Abstract: A method is provided for generating single stranded circular nucleic acid from a sample of target nucleic acid. A complex comprising a transposase and a plurality of hairpin polynucleotides is formed with each of the hairpin polynucleotides having a duplex region comprising a transposase recognition sequence. The complex is mixed with the target nucleic acid, thereby fragmenting the target nucleic acid and ligating the hairpin polynucleotides to the target nucleic acid to form hairpin-linked nucleic acid fragments, each having a nucleobase segment gap between each fragment and its corresponding hairpin polynucleotide. The hairpin-linked fragments are contacted with a ligase, thereby ligating the hairpin-linked fragments together to form single-stranded circular nucleic acid comprising a pair of opposing loops and an intervening duplex region comprising a pair of nucleobase segment gaps.

Abstract: Methods, kits, and compositions are provided herein for the generation of double stranded DNA products suitable for downstream analysis.

Abstract: Chimeric proteins comprising a sequence nonspecific single-stranded nucleic-acid-binding domain joined to a catalytic nucleic-acid-modifying domain are provided. Methods comprising contacting a nucleic acid molecule with a chimeric protein, as well as systems comprising a nucleic acid molecule, a chimeric protein, and an aqueous solution are also provided. The joining of sequence nonspecific single-stranded nucleic-acid-binding domain and a catalytic nucleic-acid-modifying domain in chimeric proteins, among other things, may prevent the separation of the two domains due to their weak association and thereby enhances processivity while maintaining fidelity.

Abstract: The present invention is directed to compositions and methods useful for the amplification of nucleic acid molecules by reverse transcriptase-polymerase chain reaction (RT-PCR). Specifically, the invention provides compositions and methods for the amplification of nucleic acid molecules in a simplified one- or two-step RT-PCR procedure using combinations of reverse transcriptase and thermostable DNA polymerase enzymes in conjunction with sulfur-containing molecules or acetate-containing molecules (or combinations of such sulfur-containing molecules and acetate-containing molecules), and optionally bovine serum albumin. The invention thus facilitates the rapid and efficient amplification of nucleic acid molecules and the detection and quantitation of RNA molecules. The invention also is useful in the rapid production and amplification of cDNAs which may be used for a variety of industrial, medical and forensic purposes.

Abstract: System, including methods, apparatus, compositions, and kits, for making and using compound droplets of a multiple emulsion to supply an amplification reagent, such as a heat-stable DNA polymerase or DNA ligase, to an aqueous phase in which the compound droplets are disposed. The compound droplets may be induced to supply the amplification reagent by heating the multiple emulsion, to achieve hot-start amplification.

Abstract: The present invention is directed to fusion proteins that can be used to assay gene transfer and expression both in vitro and in vivo. The fusion proteins contain a reporter protein, e.g. a somatostatin receptor, fused to a second protein, which may be a protein fusion tag. Alternatively, a fusion protein may be fused to a leader sequence. A leader sequence may localize an expressed protein, e.g localize a fusion protein to the cell membrane. The invention includes nucleic acids encoding the fusion proteins and methods of assaying for gene expression.

Abstract: The present invention relates to novel diagnostic, prognostic and therapeutic reagents for infection of an animal subject such as a human by Pseudomonas aeruginosa, and conditions associated with such infections, such as, for example, an acute clinical exacerbation in a cystic fibrosis (CF) subject. In particular, the present invention relates to methods for diagnosing/prognosing an infection by P. aeruginosa in a subject comprising detecting the presence or amount of one or more proteins of P. aeruginosa or a fragment or epitope thereof or an antibody thereto in a sample from the subject.

Abstract: A purified thermostable enzyme is derived form the thermophilic archaebacterium Thermococcus gorgonarius. The enzyme can be native or recombinant, retains approximately 90% of its activity after incubation for two hours at 95° C. in the presence of stabilizing agents and possesses 3?-5? proofreading exonuclease activity. Thermostable DNA polymerases are useful in many recombinant DNA techniques, especially nucleic acid amplification by the polymerase chain reaction (PCR).

Abstract: A method of altering the conformation of a polypeptide having a known three-dimensional structure is described. The method comprises attaching a first end of a polymer to a first portion of the polypeptide, attaching a second end of the polymer to a second portion of the polypeptide, and altering the mechanical tension of the polymer, thereby altering the conformation of the polypeptide. The alteration of the conformation of the polypeptide may increase or decrease the binding affinity of the polypeptide for a substrate bound by the polypeptide, or alter the catalytic rate of an enzyme. Typically, the polymer is a polynucleotide or polypeptide.

Abstract: Described herein are methods and genetically engineered cells useful for producing an altered N-glycosylation form of a target molecule. Also described are methods and molecules with altered N-glycosylation useful for treating a variety of disorders such as metabolic disorders.

Abstract: A method for efficiently constructing a cDNA library having a reduced content of cDNA clones derived from a highly expressed gene is provided. According to the method for constructing a cDNA library using a double-stranded DNA primer having oligo dT and mRNA as a template, the proportion of cDNA clones derived from a highly expressed gene in a cDNA library was decreased through coexistence with a probe having a property of binding to the mRNA of the highly expressed target gene so as to inhibit a cDNA extension reaction resulting from reverse transcriptase.

Abstract: The present invention relates to molecules and molecular complexes which comprise the active site binding pockets of JNK3 or close structural homologues of the active site binding pockets.

Abstract: The present invention provides compositions, methods, and kits relating to the protection and deprotection of molecules comprising nucleophilic groups, such as the protection and deprotection of thermostable polymerases. Also provided are methods of performing nucleic acid amplification using polymerases protected according to the invention.

Abstract: The present invention relates to a method for transfection of cells using at least one protein capable of forming nucleoprotein filaments, wherein the protein is initially modified with at least one functional component which influences one or more steps of the transfection, the nucleic acid to be transfected is then loaded with the modified protein, whereby the nucleic acid and the protein form a filament-like complex, and this complex is finally added to the cells to be transfected. The invention further relates to a transfection agent consisting of nucleoprotein filaments (NPF), with at least one nucleoprotein filament-forming protein being modified with at least one functional component for the transfection. Furthermore, the present invention relates to the use of the transfection agent according to the invention for producing a drug for gene therapeutic treatment of humans and animals.

Abstract: A novel S6 kinase, p70?S6k is described, along with methods of making and using p70?S6k protein and related nucleic acids. The invention also discloses methods of identifying agents which modulate the activity of p70?S6k protein and/or its ligands.

Abstract: A method of screening a candidate compound for ?Arrestin mediated anti-G protein coupled receptor signaling activity is comprises: (a) contacting said candidate compound to a ?Arrestin signaling complex or a constituent thereof, under conditions in which a signaling complex is formed; and then (b) detecting the presence or absence of disruption of said signaling complex, disruption of said complex indicating said compound has ?Arrestin mediated anti-G protein coupled receptor signaling activity. Compositions and kits for carrying out the method are also described.

Abstract: The present invention discloses a bladder cancer biomarker and a test method using the same. The biomarker contains at least one of the mentioned 69 compounds, such as apolipoprotein A1 (APOA1), apolipoprotein A2 (APOA2), peroxiredoxin 2 (PRDX2), heparin cofactor 2 precursor (HCII), and serum amyloid A-4 protein (SAA4), which exist in the urine specimen of a testee. The expression intensity of the biomarker can facilitate diagnosis of bladder cancer and evaluation of aggressiveness and malignancy of bladder cancer. Thereby, the physician can arrange an optimized treatment to achieve the best therapeutic effect.

Abstract: Methods and kits for amplifying a nucleic acid under isothermal conditions to form an amplified nucleic acid sequence are provided. The methods and kits comprises providing a nucleic acid template, a DNA polymerase, deoxyribonucleoside triphosphates, a primer comprising a randomized sequence, and a specific primer, and amplifying the nucleic acid template.

Abstract: The invention relates to thermostable polymerases that have polymerase activity temperatures in the range from 90.degree. C. up to 113.degree. C., such as those derived from Pyrolobus fumaria, and to polynucleotides encoding the polymerases In addition, methods of designing new thermostable DNA polymerases and methods of use thereof are also provided. The polymerases have increased activity and stability at increased pH and temperature.

Abstract: Compositions, methods, and kits for reducing strand amplification bias using bisulfite treated gDNA are provided. Methods for detecting and for quantitating the amplified bisulfite treated gDNA and inferring the presence, absence, and/or degree of methylation of target cytosine(s) in the gDNA are also provided. Such methods typically employ tailed first primer pairs, which can, but need not comprise nucleotide analogs, and optionally second primer pairs.

Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Abstract: A polynucleotide consisting of the base sequence of SEQ ID NO: 2, or a complementary strand thereto, wherein the X is one of the group being defined by the bases A, C or T. A primer and a probe specific for that polynucleotide, wherein the primer and/or probe contains at the least 10 consecutive nucleotides, and finally use of the probe for proving parkinsonism inheritance.

Abstract: Threonine is an essential amino acid for humans and in the animal feed industry where its levels in feed rations can significantly impact the cost of production of important meat sources, such as swine and poultry. Threonine as well as essential amino acids lysine and methionine are all synthesized via the aspartate family pathway. Aspartate kinase (AK) is the first enzyme in the pathway, and catalyzes the ATP-dependent phosphorylation of aspartate to form ?-aspartyl phosphate. AK constitutes the main regulatory step controlling the metabolic flux through the pathway, and is subject to end product inhibition by Lys and/or Thr. The current invention provides a method to produce a transgenic high free threonine soybean via the overexpression of feed-back-resistant AK enzymes in developing soybean plants and seeds. These modifications provide a method to enhance both plant nitrogen metabolism and crop growth performance.

Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.

Abstract: The invention relates to mutations in B-Raf gene products. The mutations described are identified in human tumours of natural origin. These mutations are associated with cancerous phenotypes and can be used as a basis for the diagnosis of cancer, cancerous cells or a predisposition to cancer in human subjects, and the development of anti-cancer therapeutics.

Abstract: Use of the large form of human 2?,5?-Oligoadenylate Synthetase (OAS3) for diagnosis, prevention and treatment of infection with positive-sense single-stranded RNA viruses and for prediction of human genetic susceptibility to positive-sense single-stranded RNA virus-related diseases.

Abstract: A method of producing a nanostructure composition from a solid powder is disclosed. The method comprises: (a) heating the solid powder, thereby providing a heated solid powder; (b) immersing the heated solid powder in a liquid in the presence of a gas medium, the liquid being colder than the heated powder, and (c) irradiating the cold liquid, the heated solid powder and the gas medium by electromagnetic radiation selected such that nanostructures are formed from particles of the solid powder and a stable gas phase is formed from the gas medium.

Abstract: The present invention relates to a method of microbial production of L-lysine from methanol and other substrates, and particularly improving the production of L-lysine from such substrates. The invention concerns a method for producing lysine in B. methanolicus, said method comprising overexpressing an aspartate kinase III (AKIII) enzyme in said B. methanolicus. In particular the method may concern introducing a nucleic acid molecule comprising a nucleotide sequence encoding an AKIII enzyme into a B. methanolicus. The invention also relates to a B. methanolicus micro-organism which overexpresses an AKIII enzyme, nucleic acid molecules which encode polypeptides having AK activity, polypeptides which have AK activity and host cells and vector systems comprising the nucleic acid molecules or vector.

Abstract: A biological process indicator is provided for validating a treatment process in which the amount or activity of a contaminant in a sample is reduced. The indicator comprises a thermostable kinase covalently linked to a biological component, with the proviso that the biological component is not an antibody. Methods of preparing the indicator, and methods of using the indicator, are also provided.

Abstract: The invention provides novel nucleic acid polymerases from strains GK24 and RQ-1 of Thermus thermophilus, and nucleic acids encoding those polymerases, as well as methods for using the polymerases and nucleic acids.

Abstract: The invention relates to molecules or molecular complexes which comprise binding pockets of TAK1 or its structural homologues. The invention relates to crystallizable compositions and crystals comprising TAK1. The present invention also relates to a data storage medium encoded with the structural coordinates of molecules and molecular complexes which comprise the TAK1 or TAK1-like ATP-binding pockets. The present invention also relates to a computer comprising such data storage material. The computer may generate a three-dimensional structure or graphical three-dimensional representation of such molecules or molecular complexes. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for and design compounds, including inhibitory compounds, that bind to TAK1 or homologues thereof.

Abstract: A polymerase activity is effectively enhanced by adding an anionic surfactant, in particular an anionic surfactant having a polyethoxyl group, to a reaction mixture containing a polymerase.

Abstract: Enzymatic pathways for production of aminoshikimate, kanosamine, intermediates, and derivatives thereof; nucleic acid encoding and cells containing the enzymes; compositions containing aminoshikimate, kanosamine, an intermediate or derivative thereof; and use of the cells and pathways for biosynthetic production of aminoshikimate, kanosamine, intermediates, and derivatives thereof.

Abstract: This invention provides for an improved generation of novel nucleic acid modifying enzymes. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the ability of the enzyme to bind and catalytically modify the nucleic acid.

Abstract: The invention relates to the use of carbamoyl synthetase 1 (CPS 1) as a humoral biomarker in in vitro methods for early diagnosis and detection, progress prognosis, the evaluation of the severity, and the progress evaluation of tumor diseases and chronic inflammatory intestinal diseases.

Abstract: The invention relates to reverse transcriptases which have increased fidelity (or reduced misincorporation rate) and/or terminal deoxynucleotidyl transferase activity. In particular, the invention relates to a method of making such reverse transcriptases by modifying or mutating specified positions in the reverse transcriptases. The invention also relates to nucleic acid molecules containing the genes encoding the reverse trancriptases of the invention, to host cells containing such nucleic acid molecules and to methods to make the reverse trancriptases using the host cells. The reverse transcriptases of the invention are particularly suited for nucleic acid synthesis, sequencing, amplification and cDNA synthesis.

Abstract: Emission ratiometric indicators of phosphoinositides comprise a fusion protein comprising a pleckstrin homology (PH) domain of Akt (also known as protein kinase B) and a “pseudoligand” containing acidic amino acid residues, which is sandwiched between resonance energy transfer (RET) pairs, such as cyan and yellow mutants of GFP (a FRET pair). Such indicators can be used, inter alia, to monitor spatiotemporal dynamics of phosphoinositides and in high throughput assays for inhibitors of PI3K, including drug screening assays.

Abstract: The present invention provides isolated nucleic acid molecules encoding a Herpesviridae thymidine kinase enzyme comprising one or more mutations, at least one of the mutations encoding an amino acid substitution located toward the N-terminus from a DRH nucleoside binding site which increases a biological activity of the thymidine kinase, as compared to unmutated thymidine kinase. Such mutations include amino acid substitutions within a Q substrate binding domain which increases a biological activity of the thymidine kinase, as compared to unmutated thymidine kinase. Within a further aspect, fusion proteins are provided which have both guanylate kinase and thymidine kinase biological properties. Also provided are vectors suitable for expressing such DNA molecules, as well as methods for utilizing such vectors.

Abstract: Compositions, systems and methods of sequencing are disclosed, where the compositions and systems include polymerase enzymes that have been genetically modified to more efficiently incorporate nucleotides including labels having a detectable properties that are released during incorporation, to augment a rate of labeled nucleotide incorporation, to augment a rate of pyrophosphate release, or to augment two or more of these properties and rates. Also disclosed are terminally labeled and dual labeled nucleotides, and click-chemistry based methods of synthesizing the same.

Abstract: The invention establishes a technology that allows non-specific amplification to be inhibited during nucleic acid amplification in an isothermal amplification reaction, such that the amplification efficiency is increased. The invention is a extreme thermophile single-stranded DNA binding mutant protein, having an amino acid sequence that expresses a function that can contribute to increasing an amplification efficiency of a template nucleic acid in an isothermal amplification reaction system that uses a strand displacement polymerase, and having in its amino acid sequence a mutation site where a mutation involving at least one of deletion, substitution, addition, and insertion of one or more amino acids in amino acid sequence of extreme thermophile single-stranded DNA binding protein has occurred, and a method of use thereof.

Abstract: The present invention relates to methods for diagnosis or monitoring of viral infection by detecting the presence of transrenal viral nucleic acids or nucleic acids of viral origin in urine sample, with or without isolation of nucleic acids from a urine sample. The analysis of the nucleic acids is performed through hybridization of the nucleic acids with specific probes, or through a chain amplification reaction with specific primers. The methods are applicable to all viral pathogenic agents, including RNA, DNA, episomal, or integrated viruses.

Abstract: It was found that a fragment of native Thermus aquaticus DNA polymerase (TaqWT) lacking 288 N-terminal amino acids (Taq?288) possesses an increased thermostability over TaqWT, Taq?279, and Taq?289. The present invention therefore provides Taq?288, recombinant expression vectors encoding the same or derivatives thereof, as well as purification protocols for Taq?288. The invention also encompasses kits containing Taq?288 as well as the use of Taq?288 and kits containing Taq?288. In addition, the invention encompasses methods for the sequencing a nucleic acid template and methods for amplifying a target nucleic acid.

Abstract: The present invention relates to nucleic acid inhibitors, compositions and method for enhancing synthesis of nucleic acid molecules. In a preferred aspect, the invention relates to inhibition or control of nucleic acid synthesis, sequencing or amplification. Specifically, the present invention discloses nucleic acids having affinity for polypeptides with polymerase activity for use in such synthesis, amplification or sequencing reactions. The nucleic acid inhibitors are capable of inhibiting nonspecific nucleic acid synthesis under certain conditions (e.g., at ambient temperatures). Thus, in a preferred aspect, the invention relates to “hot start” synthesis of nucleic acid molecules. Accordingly, the invention prevents, reduces or substantially reduces nonspecific nucleic acid synthesis. The invention also relates to kits for synthesizing, amplifying, reverse transcribing or sequencing nucleic acid molecules comprising one or more of the nucleic acid inhibitors or compositions of the invention.

Abstract: The present invention relates to crystalline Mnk-1 and Mnk-2 kinases and, in particular, to the crystal structure of Mnk-1 and Mnk-2 kinase domain.

Abstract: The present invention relates to a composition comprised of AKAP12 (A-Kinase anchoring protein 12) and to uses of AKAP12 mutant zebrafish as an animal model. More particularly, the following characteristics are noted in the present AKAP12 mRNA knockdown zebrafish: crooked or shortened tail, inability to move normally, non-uniform micro-vasculature in the brain, and change in heart shape with non-uniform and weak heartbeats. It also has various circulatory and genetic defects, such as hemorrhage from the ventricles of the heart, brain, and retina. All of these defects can be cured with AKAP12 injection. Therefore, AKAP12 can be used as an active component for a composition to prevent and heal circulatory and genetic defects that are caused by AKAP12 deficiency, and as a hemorrhage inhibitor. Further, the AKAP12 deficient mutant zebrafish can be useful as an animal model for verification of effectiveness of treatment for genetic defects in the circulatory system.

Abstract: The present invention concerns an antibody specific for human ALK (Anaplastic Lymphoma Kinase), in particular a scFv, a nucleic acid sequence encoding it, its production and its use as a pharmaceutical or for diagnostic purposes. Said antibody is suitable for the local treatment of tumors, in particular glioblastoma.

Abstract: A sucrose phosphorylase (SP) having improved thermostability obtained by modifying a natural SP and a method for producing the SP having improved thermostability is provided. This SP having improved thermostability has an amino acid residue which is different from that of the natural sucrose phosphorylase, in at least one position selected from the group consisting of a position corresponding to position 14, a position corresponding to position 29 and a position corresponding to position 44 in motif sequence 1; a position corresponding to position 7, a position corresponding to position 19, a position corresponding to position 23 and a position corresponding to position 34 in motif sequence 2; and a position corresponding to position 19 in motif sequence 3, and wherein the enzyme activity of the SP having improved thermostability at 37° C., after heating the SP having improved thermostability in 20 mM Tris buffer (pH 7.0) at 55° C.

Abstract: Coexpression of a polyhydroxyalkanoic acid synthase and a either a fatty acid:acyl-CoA transferase or an acyl-CoA synthetase in cells enables the biosynthesis of polyester materials. Plasmids, bacteria, materials, and methods for the preparation of polyesters are disclosed.

Abstract: The invention relates to methods and compositions for regulation of GSK3? activity. The invention provides phosphorylated GSK3? polypeptides and antibodies that recognize such polypeptides. The invention further includes methods for treating disorders that are associated with elevated or reduced GSK3? activity.

Abstract: The present patent application discloses a method of identifying or validating a compound that modulates the phosphorylation-dependent activity of a target protein or protein complex, where the target protein or protein complex activity is regulated by phosphorylation, as well as the use of identified compounds for the production of a pharmaceutical preparation especially for the treatment of cancer, insulin resistance and diabetes.