Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.

Abstract: Compositions are provided that include a plurality of small molecules selected from the group consisting of an amide, urea or acetone having a molecular weight less than 300 g/mol; and dNTPs and a polymerase in a buffer suitable for use as an amplification buffer. Methods of use of the compositions are also described for reducing non-template DNA amplification.

Abstract: Disclosed are methods and kits for endonuclease-assisted DNA amplification reaction using decontaminated primer solutions that are pre-treated with a nuclease. Nucleic acid amplification assays that employ nuclease-resistant, inosine-containing primers, endonuclease V enzymes to introduce a nick into a target DNA comprising at least one inosine, and a DNA polymerase to generate amplicons of a target DNA are also disclosed.

Abstract: Methods, microbial strains and reaction mixtures for cell-free synthesis of polypeptides are provided. The methods of the invention utilize a reaction mixture comprising microbial cell extracts that are modified in the protein component relative to an extract from a native cell. The modification may be one or both of (i) increased levels of proteins that increase synthetic yield; and (ii) decreased levels of proteins that decrease synthetic yield. The modification may result from a genetic modification of the microbial cell, or from ex vivo supplementation or depletion of an extract.

Abstract: A method for improving the thermostability of a protein includes introducing, into the protein, two or more amino acid substitutions selected from the group consisting of: (i) substitution of an arginine residue for a lysine residue, (ii) substitution of a threonine residue for a serine residue, and (iii) substitution of an alanine residue for a serine residue.

Abstract: The present invention relates to plant cells and plants, which are genetically modified, whereby the genetic modification leads to an increase in the activity of a starch-phosphorylating OK1 protein in comparison to the corresponding wild type plant cells or wild type plants that have not been genetically modified. In addition, the present invention concerns means and methods for the manufacture of such plant cells and plants. These types of plant cells and plants synthesise a modified starch. Therefore, the present invention also concerns the starches synthesised from the plant cells and plants according to the invention, methods for manufacturing these starches, and the manufacture of starch derivatives of these modified starches, as well as flours containing starches according to the invention. Furthermore, the present invention also relates to nucleic acids, coding starch-phosphorylating OK1 proteins, vectors, host cells, plant cells, and plants containing such nucleic acid molecules.

Abstract: The present invention provides thermostable enzymes, such as DNA polymerases and restriction endonucleases, that are substantially free from contamination with nucleic acids. The invention also provides methods for the production of these enzymes, and kits comprising these enzymes which may be used in amplifying or sequencing nucleic acid molecules, including through use of the polymerase chain reaction (PCR).

Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.

Abstract: The invention relates to isolated nucleic acid molecules and to host cells comprising such nucleic acid molecules. Moreover, the invention relates to a polypeptide having PIM-3 activity and having a definite amino acid sequence, as well as to the use of PIM-3 as a screening agent for identifying anti-type 2 diabetes mellitus drugs and for preparing a medicament for the treatment of insulin resistance or type 2 diabetes mellitus.

Abstract: The present invention provides a process for the production of nucleic acid encoding a target protein, which comprises: (a) providing an array of RNA or DNA molecules including one or more encoding the target protein; (b) generating a target protein from the array to form RNA-protein or DNA-protein complexes in which the RNA or DNA molecule is non-covalently or covalently bound to the complex; (c) separating the complexes into compartments wherein most or all of the compartments contain no more than one complex; (d) subjecting the complexes to reaction conditions which allow target protein activity; and (e) selecting nucleic acid encoding the target protein on the basis of the activity associated therewith, wherein when the complex is a DNA-protein complex in which the DNA is non-covalently bound, step b) is performed in the absence of separate compartments for each complex.

Abstract: The present invention relates to an engineered polymerase with an expanded substrate range characterised in that the polymerase is capable of incorporating an enhanced occurrence of detection agent-labelled nucleotide analogue into nucleic acid synthesised by that engineered polymerase as compared with the wild type polymerase from which it is derived.

Abstract: The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

Abstract: The present invention relates to methods of assembling a plurality of genetic units to form synthetic genetic constructs. This method involves appending universal adapter oligonucleotides and flexible adapter oligonucleotides to the 5? and 3? ends of separate genetic units to be assembled to form separate dual extended genetic units. The dual extended genetic units are assembled together via homologous recombination between the flexible adapter oligonucleotide portions of the dual extended units to form synthetic genetic constructs. The present invention further relates to synthetic genetic constructs formed using the methods of the present invention, and vectors, cells, and organisms containing such synthetic genetic constructs.

Abstract: The present invention deals with a method of producing 2,4-dihydroxybutyric acid (2,4-DHB) by a synthetic pathway comprising the transformation of malate in 4-phospho-malate using a malate kinase, said 4-phospho-malate being transformed in malate-4-semialdehyde using a malate semialdehyde dehydrogenase and said malate-4-semialdehyde being transformed in 2,4-DHB using a DHB dehydrogenase.

Abstract: Non-hydrophobic beads and methods to reversibly bind, normalize, store and in situ deliver primers to reactions including PCR. Also provided are instructions for preparing the beads. In the presence of an appropriate binding buffer, a bead can be used to bind and desalt primers from a crude solution of DMT-off primers. In the presence of an appropriate binding buffer, a bead can be used to bind and purify primers from a crude solution of DMT-on primers. A bead may bind a picomolar amount of DMT-on primers from a solution containing a plurality of crude DMT-on primers. Upon detritylation and washing, the resulting DMT-off primer bound bead may be used in PCR. Primers are released from the bead upon cycling the temperature. Primer bound beads are coated or silanized with hydrophobic reagents which ensures a gradual release of primers during the thermal cycling of the PCR reaction. Coating or silanization in turn enhances primer stability and long term storage.

Abstract: The present invention relates to mutant DNA polymerases that exhibit reduced discrimination against labeled nucleotides into polynucleotides. The DNA polymerases of the invention have at least one mutation in the nucleotide label interaction region of the enzyme such the mutation results in reduced discrimination against labeled nucleotides. The nucleotide label interaction regions are located at portions of the O-helix, the K-helix, and the inter O-P helical loop of Taq DNA polymerase or analogous positions in other DNA polymerases. The invention also provides polynucleotides encoding the mutant DNA polymerases, optionally including expression vectors for mutant polymerase recombinant production, and further optionally including host cells containing the polynucleotides. Numerous methods of using the subject DNA polymerases are provided, including uses for chain termination sequencing and PCR.

Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.

Abstract: The present invention relates to a composite metastasis score (“cMS”) based on expression of a 14-gene molecular signature (referred to as a metastasis score, or “MS”) in combination with progesterone receptor (PR) expression that is useful for predicting breast cancer metastasis. In preferred embodiments, the cMS is determined by applying weighted coefficients to MS and PR. The present invention provides methods and reagents for detecting and profiling the expression levels of these genes, and methods of using the expression level information for predicting risk of breast cancer metastasis, among other embodiments.

Abstract: The present invention relates to a variant archaeal DNA polymerase having a modified amino acid sequence of a wild-type amino acid sequence, the modified sequence being in the amino-terminal amino acids that comprise a uracil-binding pocket in the wild-type polymerase whereby the variant polymerase has reduced affinity for uracil than the wild-type polymerase. Such variant polymerases may be usefully employed in biological assay systems such as the polymerase chain reaction.

Abstract: The invention provides a method of improving the efficiency of establishment of induced pluripotent stem cells by increasing, in a nuclear reprogramming step of somatic cell, the level of activated form of one or more proteins selected from the group consisting of Ras family members, PI3 kinase, RalGEF, Raf, AKT family members, Rheb, TCL1 and S6K. The invention also provides a method of producing induced pluripotent stem cells by contacting a somatic cell with a nuclear reprogramming substance and one or more of such proteins and nucleic acids that encode such proteins. The invention further provides an induced pluripotent stem cell that has an exogenous nucleic acid encoding such a protein, as well as agents for use in the aforesaid methods.

Abstract: Disclosed is a T7 RNA polymerase mutant having improved thermal stability and/or specific activity in comparison with wild-type T7-like bacteriophage RNA polymerase, wherein at least one amino acid residue corresponding to at least one of the amino acid residues selected from the group at least consisting of glutamine at position 768, lysine at position 179 and valine at position 685 of the amino acid sequence that composes wild-type T7 RNA polymerase shown in SEQ ID NO: 6, is substituted with another amino acid.

Abstract: The invention provides methods of removing nucleic acid contamination from reverse transcription reactions and hot-start PCR, wherein said hot-start PCR is a barrier hot-start PCR set up and/or involves a hot-start DNA polymerase, which methods comprise use of a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA. The invention further provides a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA, nucleic acids encoding said DNase and kits or compositions comprising said DNase or said nucleic acid.

Abstract: Compositions of novel polymerase variants and methods of identifying, making and using these novel polymerases are described. The variants have been shown to have advantageous properties such as increased thermostability, deoxyuridine nucleoside triphosphate tolerance, salt tolerance, reaction speed and/or increased reverse transcriptase properties. Uses for these improved enzymes have been demonstrated in isothermal amplification such as LAMP. Enhanced performance resulting from the use of these variants in amplification has been demonstrated both in reaction vessels and in dedicated automated amplification platforms.

Abstract: An isolated polypeptide having fast elongating polymerase activity. Also provided are kits containing the isolated polypeptide and isolated polynucleotides encoding the isolated polypeptide.

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: The invention provides variant phytase enzymes having increased thermal stability relative to their counterpart parent enzymes. The modifications to the enzymes include both single substitutions and various combinations of substitutions that provide improved stability and activity. The invention further provides nucleic acids encoding the variant phytase enzymes, host cells and vectors containing and expressing them, as well as feed compositions useful for providing improved nutrition, particularly with respect to the bioavailability of dietary phosphate, calcium, iron and zinc, among others.

Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.

Abstract: Methods for making cDNA molecules, for amplification of RNA by PCR and for preparation of cDNA libraries are provided. Kits for making cDNA molecules also are provided. Compositions are also provided comprising mixtures of reagents, including reverse transcriptases, buffers, cofactors and other components, suitable for immediate use in conversion of RNA into cDNA and RT PCR without dilution or addition of further components. These compositions are useful, alone or in the form of kits, for cDNA synthesis or nucleic acid amplification (e.g., by the Polymerase Chain Reaction) or for any procedure utilizing reverse transcriptases in a variety of research, medical, diagnostic, forensic and agricultural applications.

Abstract: The present invention provides a high-throughput sequencing method for methylated DNA, and use thereof. Particularly, the present invention provides a high-throughput sequencing method for methylated DNA, which combines methylated DNA immunoprecipitation, removal of repetitive sequences, and bisulfite treatment. The site of sequencing library will be decreased, and the cost will be reduced by using the method disclosed in the present invention.

Abstract: The invention relates to a polypeptide having a mutation at one or more position corresponding to T219 of SEQ ID NO: 55, wherein the polypeptide has at least 50% sequence identity with SEQ ID NO: 55, and wherein the polypeptide has permease activity.

Abstract: The present invention provides an epidermal growth factor receptor variant-de4 EGFR protein. The variant lacks the fourth exon of the epidermal growth factor receptor, and promotes tumor cell invasion/metastasis. The present invention also provides an encoding gene for the variant and a method of producing the variant by means of recombination technology.

Abstract: A DNA polymerase chimera comprising an amino-terminal (N-terminal) region encoding a ?29 type DNA polymerase and a carboxyl-terminal (C-terminal) region comprising at least one HhH domain which are bound by a connecting amino acid sequence is disclosed along with and the use thereof for replicating, amplifying or sequencing a template DNA. Also disclosed is a method for replicating, amplifying or sequencing a deoxyribonucleic acid with a DNA polymerase chimera and kits for carrying out the methods.

Abstract: Compositions and methods are provided for inhibiting a polymerase from replicating non target DNA at a temperature below the amplification reaction temperature. The inhibitor is a synthetic nucleic acid which is single stranded but folds to form at least one double stranded region designed to melt at a temperature which is lower than the amplification reaction temperature, and at least one single stranded region where the single stranded region at the 5? end contains at least one uracil or inosine and optionally a sequence at the 3? end contains one or more derivative nucleotide or linkages.

Abstract: A novel gene encoding P. pastoris orotate-phosphoribosyl transferase (URA5) is disclosed. Methods for producing and selecting yeast strains capable of stable genetic integration of heterologous sequences into the host genome are also provided.

Abstract: The present invention provides materials and methods useful for error correction of nucleic acid molecules. In one embodiment of the invention, a first plurality of double-stranded nucleic acid molecules having a nucleotide mismatch are fragmented by exposure to a molecule having unidirectional mismatch endonuclease activity. The nucleic acid molecules are cut at the mismatch site or near the mismatch site, leaving a double-stranded nucleic acid molecule having a mismatch at the end or near end of the molecule. The nucleic acid molecule is then exposed to a molecule having unidirectional exonuclease activity to remove the mismatched nucleotide. The missing nucleotides can then be filled in by the action of, e.g., a molecule having DNA polymerase activity. The result is double-stranded nucleic acid molecules with a decreased frequency of nucleotide mismatches.

Abstract: A method is disclosed for improved isothermal amplification of nucleic acids comprising the step of release of an essential component from a matrix under predetermined conditions. Furthermore, the invention relates to a kit comprising mesophilic enzyme and a matrix with embedded essential components for isothermal amplification. A composition comprising a matrix and a mesophilic enzyme and a method for embedding a mesophilic enzyme are disclosed as well.

Abstract: The invention relates to modified T7-related RNA polymerases and methods of use thereof. In some embodiments, the invention relates to modified T7-related RNA polymerases that transcribe RNA with reduced abortive cycling and increased efficiency compared with native T7-related RNA polymerases.

Abstract: Methods and compositions for modulating GABA release in a subject are provided. A preferred embodiment provides a composition containing an effective amount of an ErbB4 ligand to enhance or promote GABA release, i.e., GABAergic transmission. The ErbB4 ligand can be an agonist ligand or an antagonist ligand depending on the disorder to be treated. Methods for treating neurological disorders are also provided. Representative disorders that can be treated include, but are not limited to schizophrenia, epilepsy, depression and anxiety, insomnia, stroke, pain, bipolar, autism, or a combination thereof. By increasing GABA release a sedative effective can be induced in the subject. Methods for inducing a stimulatory effect in a subject are also provided. In these methods, an effective amount of an ErbB4 antagonist ligand is administered to the subject to reduce or inhibit GABA release in the subject.

Abstract: The present invention provides thermostable enzymes, such as DNA polymerases and restriction endonucleases, that are substantially free from contamination with nucleic acids. The invention also provides methods for the production of these enzymes, and kits comprising these enzymes which may be used in amplifying or sequencing nucleic acid molecules, including through use of the polymerase chain reaction (PCR).

Abstract: Disclosed are methods for the enhancement of the reactivation of thermostable reversibly inactivated enzymes comprising reactivating at least one thermostable reversibly inactivated enzyme in the presence of one or more nitrogen containing compounds.

Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. 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 present disclosure provides methods and compositions for performing nucleic acid reactions, such as the reverse transcriptase-polymerase chain reaction (RT-PCR).

Abstract: A primer for the amplification of a DNA template comprising a protelomerase target sequence, particularly for production of closed linear DNA, which primer is capable of specifically binding to a palindromic sequence within a protelomerase target sequence and priming amplification in both directions.

Abstract: Oligonucleotide primer useful for synthesizing a cDNA copy of HIV-1 nucleic acids from a broad range of HIV-1 subtypes, including M group and O group variants.

Abstract: Methods and kits for efficient amplification of nucleic acids are provided. The disclosure generally relates to methods and kits for nucleic acid amplification of target nucleic acids of interest. The methods described herein promote the synthesis of the target nucleic acid (i.e., template nucleic acid) by reducing the production of undesirable primer-dimer structures and chimeric nucleic acid products during the amplification process by using novel modified primers.

Abstract: Described herein are truncated EGF receptor polypeptides, nucleic acids encoding them, and methods of using them to help select a method of treatment for an EGFR-related cancer, to predict clinical outcome, and to detect micrometastases or minimal residual disease. High EGFR expression and phosphorylated EGFR predicts poor survival in head and neck cancer patients, but does not correlate with advanced stage disease. In our studies, we determined that clinical biological correlates are likely to be more accurate when different aspects of EGFR are evaluated in combination. We analyzed EGFR phosphorylation, expression and mutations in 60 primary head and neck tumors. We not only found that head and neck tumors with either truncated or activated EGFR tend to have higher tumor and nodal stage, but also discovered three EGFR truncations.

Abstract: The present invention relates to a method for amplifying a template nucleic acid, wherein the method comprises amplifying said template nucleic acid using the helicase dependent amplification (HDA) reaction in the presence of a nicking endonuclease, and wherein said template nucleic acid comprises a sequence recognized by said nicking endonuclease or a sequence recognized by said nicking endonuclease is introduced into the template nucleic acid during the HDA reaction. The invention further pertains to a kit for amplifying a nucleic acid, comprising a nicking endonuclease, a helicase and a DNA polymerase.

Abstract: The present invention is directed to compositions of matter useful for the diagnosis and treatment of tumor in mammals and to methods of using those compositions of matter for the same.

Abstract: A method for amplification of a target DNA, comprising the steps of (i) transferring a liquid with a first volume comprising at least one or more living cells into a vessel (ii) adding to said vessel a PCR reaction buffer with a second volume, whereas said second volume is at least 2× as large as said first volume (iii) lysing said at least one or more living cells within said vessel by means of incubation for at least 1 Minute at at least 90° C., and (iv) amplifying said target by means of a polymerase chain reaction without performance of an intermediate purification step.

Abstract: Molecular signatures that function as very sensitive diagnostic biomarker for myocarditis, heart disease and disorders thereof, are identified.