Abstract: The present disclosure provides systems, devices and methods associates with processing and analyzing samples for molecular diagnostics. The system may process samples using assay cartridges including sample preparation modules and PCR modules. The system may include thermal cycler modules and optics modules to detect the specific nucleic acid sequences in the samples.

Abstract: A method of examining a water supply for microbial contamination involves contacting a water supply with a novel reagent having high specificity for a Legionella microbial species, wherein said reagent does not cross-react, or minimally cross-reacts, with a microbial species other than Legionella. The method further involves detecting, or measuring, a contaminating concentration of a Legionella species in the water supply. Useful reagents comprise at least one nucleotide sequence primer comprising a primer sequence selected from SEQ ID NO: 3-10 or a combination of such primer sequences. The increased specificity of such reagents permits more sensitive detection of microbial contamination.

Abstract: A method for the production of nucleic acid encoding a target protein. The method 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 provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

Abstract: The present invention relates to chimeric immune receptor molecules for reducing or eliminating tumors. The chimeric receptors are composed a C-type lectin-like natural killer cell receptor, or a protein associated therewith, fused to an immune signaling receptor containing an immunoreceptor tyrosine-based activation motif. Methods for using the chimeric receptors are further provided.

Abstract: The present invention provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

Abstract: In accordance with the present invention, there are provided functionally modulated tool receptors which are useful for drug discovery and development. In certain aspects and embodiments as described herein, a sophisticated and powerful approach has been designed that allows the rapid development of enhanced receptors, while simultaneously exploring millions of possibilities for improved properties with respect to such properties as protein expression, homogeneity, stabilization, conformational and activation pathway selectivity, antigenicity, immunogenicity, and the like. Indeed, the new methodology described herein represents a breakthrough by leveraging a full range of combinatorial amino acid replacements, in multiple positions simultaneously, in order to generate modified membrane-spanning proteins.

Abstract: The present invention provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

Abstract: The invention provides to PKN1 gene fusions, PKN1 fusion proteins, and fragments of those genes and polypeptides. The invention further provides methods of diagnosing and treating diseases or disorders associated with PKN1 fusions, such as conditions mediated by aberrant PKN1 expression or activity, or over expression of PKN1.

Abstract: Non-FRET-based fusion protein reporter molecules are provided that can be used to monitor histone modifications in living cells. Transgenic animals, particularly non-human mammals, whose genomes comprise an expression cassette encoding a non-FRET-based fusion protein reporter, are also provided. Methods of using the fusion reporter molecules for diagnosing histone-modification-associated disorders and to identify candidate pharmaceutical agents that effect histone modification in cells and tissues are also provided.

Abstract: This disclosure provides systems and methods for attaching nanopore-detectable tags to nucleotides. The disclosure also provides methods for sequencing nucleic acids using the disclosed tagged nucleotides.

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: Methods and devices are provided for manipulating droplets on a support using surface tension properties, moving the droplets along a predetermined path and merging two droplets together enabling a number of chemical reactions. Disclosed are methods for controlling the droplets volumes. Disclosed are methods and devices for synthesizing at least one oligonucleotide having a predefined sequence. Disclosed are methods and devices for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides having a predefined sequence.

Abstract: A composition for hot-start reverse transcription reaction and a composition for reverse transcription PCR are disclosed. The composition is obtained by adding pyrophosphate and pyrophosphatase to an aqueous solution containing reaction buffer solution, MgCl2, four kinds of dNTPs, and reverse transcription polymerase in a single reaction tube. The composition for hot-start reverse transcription reaction is obtained by freezing or drying the composition. The composition show increased stability and long-term storage stability. Also, disclosed is a composition that additionally includes DNA polymerase, and, thus, enables a hot-start reverse transcription reaction and a PCR reaction to be sequentially performed. A method for amplifying a nucleic acid by using the composition. The composition of the invention can be conveniently and effectively used in multiplex reverse transcription PCRs or real-time quantitative reverse transcription PCR.

Abstract: The present invention relates to a vaccine comprising the insertion of three genes, the TAA/ecdCD40L EA1 and CDA, driven by promoters L-plastin/cytosinedeaminase and CMV as a three gene, three transcription unit oncolytic virus as a conditionally replication competent adenoviral vector which replicates only in tumor cells. In these transcription units, the E1A gene of the adenoviral vector as well as the cytosine deaminase gene are under the control of the L-plastin promoter, while the TAA/ecdCD40L transcription unit is under control of a the CMV promoter.

Abstract: Stabilized reverse transcriptase fusion proteins including a thermostable reverse transcriptase connected to a stabilizer protein are described. Attaching the stabilizer protein to the thermostable reverse transcriptase stabilizes the fusion protein and can aid in its purification, provide increased solubility, allow for longer storage, or allow the fusion protein to be used under more rigorous conditions such as higher temperature. The stabilized reverse transcriptase fusion protein can also include a linker between the stabilizer protein and the thermostable reverse transcriptase. The stabilized reverse transcriptase fusion proteins are suitable for use in nucleic acid amplification methods such as the reverse transcription polymerase chain reaction and other applications involving cDNA synthesis.

Abstract: Described herein are methods, compositions and kits directed to the detection of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g., translocations, insertions, inversions and deletions. Samples containing dysregulated gene(s) of interest may show independent expression patterns for the 5? and 3? regions of the gene. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5? portion of a target gene relative to the 3? region of the target gene.

Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.

Abstract: Methods for identifying patient specific driver mutations are provided. The methods provided identify specific patient derived markers associated with aberrant signal transduction pathways, in biological samples of a cancer patient.

Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.

Abstract: The embodiments described herein pertain to cells, and methods for preparing cells, that can be used as biocatalysts by altering enzymes that compete for a substrate or product of a pathway of interest such that the targeted enzyme is sensitive to a site-specific protease, which protease is expressed but relocated in the cell to a site where it is not in contact with the targeted enzyme in the intact cell. Upon cell lysis, the protease contacts the target enzyme, which is then inactivated by protease cleavage.

Abstract: Disclosed are methods of detecting enzymatic activity on a fluorophore-labeled substrate using by monitoring the fluorescence lifetime of the fluorophore.

Abstract: The present disclosure relates to methods for the diagnosis and evaluation of neoplastic disorders, particularly non-small cell lung cancer. Assays are described in which patient test samples are analyzed for the presence of one or more specific EML4-ALK fusion genes associated with neoplastic disorders.

Abstract: Compositions and methods for modifying genetic material are provided. One embodiment provides aptamers capable of binding to a site-specific DNA binding moiety to facilitate the exchange of homologous genetic information between a donor molecule and the desired target locus (aptamer-guided gene targeting or AGT). One embodiment provides an oligonucleotide containing a aptamer, preferably a DNA aptamer at the 5? end. The oligonucleotide also contains a region of homology, also referred to as donor DNA, to a desired nucleic acid, locus, or gene. The DNA binding moiety can be a nucleic acid, a protein, or a complex of proteins. In a preferred embodiment the DNA binding moiety is a homing endonuclease that cuts DNA to facilitate the modification of the DNA by the donor DNA.

Abstract: A mutant MMLV reverse transcriptase that may have an improvement in one or more properties is provided. For example, the present reverse transcriptase is believed to be more efficient relative to other commercially available MMLV reverse transcriptase variants, particularly for templates with a higher GC content.

Abstract: The technology provided herein relates to novel variants of DNA-Polymerases exhibiting high termo-stability as well as a strong strand displacement activity; to nucleic acid molecules encoding said DNA-Polymerases, vectors, host cells containing the nucleic acids and methods for preparation and producing such enzymes; compositions comprising at least one of the DNA-Polymerases; and methods for using such enzymes in DNA sequencing and/or DNA amplification processes.

Abstract: In some embodiments, the disclosure relates generally to methods as well as related compositions, systems, kits and apparatus comprising linking proteins to target compounds and/or to locations of interest using tethers. For example, the tether can be used to link the protein to a target compound, for example, to link an enzyme to a substrate. Similarly, the tether can be used to link the protein at or near a desired location on a surface. In one group of embodiments, the tether includes a polynucleotide and the target compound or location on the surface includes another polynucleotide that is capable of hybridizing to the tether. In such embodiments, the tether can be used to link the protein to the target compound or location using nucleic acid hybridization.

Abstract: The invention provides methods and compositions for detecting and/or quantifying vector backbone in a nucleic acid preparation comprising a polynucleotide of interest using amplification assays that amplify a junction located between the polynucleotide of interest and the vector backbone, under conditions whereby amplification can occur, wherein the junction comprises a recognition site for a nuclease, and detecting the absence of an amplification product, whereby the absence of the amplification product indicates low or no vector backbone and/or quantifying the amount of amplification product to determine the amount of vector backbone in the nucleic acid preparation.

Abstract: The present invention is in the fields of molecular and cellular biology. The invention is generally related to reverse transcriptase enzymes and methods for the reverse transcription of nucleic acid molecules, especially messenger RNA molecules. Specifically, the invention relates to reverse transcriptase enzymes which have been mutated or modified to increase thermostability, decrease terminal deoxynucleotidyl transferase activity, and/or increase fidelity, and to methods of producing, amplifying or sequencing nucleic acid molecules (particularly cDNA molecules) using these reverse transcriptase enzymes or compositions. The invention also relates to nucleic acid molecules produced by these methods and to the use of such nucleic acid molecules to produce desired polypeptides. The invention also concerns kits comprising such enzymes or compositions.

Abstract: The present invention provides a method for screening compounds for their ability to inhibit autophosphorylation of Janus kinase 3 in the absence of any additional substrate. The present invention also provides a method for screening compounds that bind to Janus kinase 3 domains other than the kinase domain, to identify synthetic or natural compounds including biomolecules, that modulate Janus kinase 3 activity. This invention also describes a multi-component screening kit composed of purified recombinant Janus kinase 3 proteins and recombinant phosphorylated Janus kinase 3 fusion proteins including, one or more phosphorylated or non-phosphorylated domain-deleted Janus kinase 3 fusion proteins.

Abstract: An isolated peptide is disclosed which comprises an amino acid sequence being at least 80% homologous to the sequence as set forth in SEQ ID NO: 1 (PERYQNLSPV), the isolated peptide comprising a nuclear targeting activity, the peptide being no longer than 20 amino acids.

Abstract: A method for the production of nucleic acid encoding a target protein. The method 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: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogs, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.

Abstract: The invention provides novel reverse transcriptases (RTs) with desirable properties such as increased thermostability, increased thermoreactivity and/or increased resistance to inhibitors. In certain embodiments, the invention provides methods of producing, amplifying and/or sequencing nucleic acid molecules (particularly cDNA molecules) using kits, compositions and/or reactions mixtures containing such novel reverse transcriptase enzymes.

Abstract: The technology relates in part to methods and compositions for isothermal amplification of nucleic acids.

Abstract: A composition having nucleic acid polymerase activity, which comprises an active nucleic acid polymerase and an excess amount of a non-functional mutant nucleic acid polymerase protein, wherein the non-functional mutant nucleic acid polymerase protein stabilizes the active nucleic acid polymerase against loss of polymerase activity.

Abstract: The present invention relates to a reverse transcriptase having improved thermostability, more precisely a mutant reverse transcriptase with improved thermostability by substitution of one or more amino acids selected from the group consisting of the 63rd glutamine (Q63), the 264th lysine (K264), the 295th lysine (K295), the 306th threonine (T306), the 346th glutamic acid (E346), the 408th proline (P408), the 438th histidine (H438), and the 454th asparagin (N454) of the amino acid sequence of M-MLV originated reverse transcriptase represented by SEQ. ID. NO: 1 with other amino acids. The mutant reverse transcriptase of the present invention demonstrates excellent thermostability, compared with the wild type reverse transcriptase. Therefore, it is advantageous to obtain the target cDNA with stable reverse transcription activity even in the presence of RNA that can form the stable secondary structure at a high temperature.

Abstract: Reverse transcriptase mixtures with improved storage stability are provided.

Abstract: This disclosure provides, among other things, a composition comprising: a 5? exonuclease; a strand-displacing polymerase; and optionally a single strand DNA binding protein and/or a ligase. A method for polynucleotide assembly to form a synthon, as well as a kit for performing the same, are also described.

Abstract: Certain embodiments provide a GPCR fusion protein. In particular embodiments, the GPCR fusion protein comprises: a) a G-protein coupled receptor (GPCR); and b) an autonomously folding stable domain, where the autonomously folding stable domain is N-terminal to the GPCR and is heterologous to the GPCR. The GPCR fusion protein is characterized in that is crystallizable under lipidic cubic phase crystallization conditions. In certain embodiments, the GPCR fusion protein may be crystallizable in a complex with a G-protein or in a complex with an antibody that binds to the IC3 loop of the GPCR.

Abstract: Provided herein are methods of producing a genetically modified cell by introducing a polydnavirus delivery construct to a target cell. The polydnavirus delivery construct can comprise an exogenous nucleic acid to form a genetically modified cell comprising the exogenous nucleic acid. Also provided are polydnavirus delivery constructs comprising an exogenous nucleic acid, as well as polydnavirus virions and genetically modified cells comprising the same. Further provided are in vitro methods of identifying a transformed cell. The methods comprise introducing a vector comprising a nucleotide sequence encoding a glc polypeptide to an adherent cell and cultivating the cell under conditions that allow for the expression of the glc polypeptide. Expression of the glc polypeptide results in a transformed cell that is identified by a loss of adherency.

Abstract: Mutants of bacteriophage phi29 DNA polymerase with increased protein stability and increased half-life, compared to wild type DNA polymerase. The disclosed mutants are more stable in reaction mixtures with or without DNA. The inventive phi29 DNA polymerase mutants generate more amplification product. The inventive phi29 DNA polymerase mutants amplify genomic DNA with less bias compared to wild type DNA polymerase. Selected mutations increase the affinity of polymerase for DNA template.

Abstract: The present invention provides cold shock protein-containing compositions for improved DNA synthesis reactions with improved reactivity, methods for synthesizing DNA using such compositions, kits for use in such methods, and DNA compositions yielded by such methods. The present invention further provides cold shock protein-containing compositions for the identification of endoribonuclease cleavage sites, methods for identifying endoribonuclease cleavage sites using such compositions, and kits for use in such methods.

Abstract: The invention provides nucleic acids and polypeptides for a nucleic acid polymerase from a thermophilic organism, Thermus scotoductus. The invention also provides methods for using these nucleic acids and polypeptides.

Abstract: An isolated mutant Tfi DNA polymerase having a D144A point mutation. This polymerase may be used in methods including, but not limited to, nucleic acid synthesis, DNA sequencing, nucleic acid amplification and cDNA synthesis.

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: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: This disclosure provides peptides, polypeptides, fusion polypeptides, compositions, and methods for enhancing or increasing the stability of a polypeptide (e.g., Taq polymerase). Such peptides, polypeptides, fusion polypeptides, or compositions include polypeptides linked to a peptide tag that enhances the stability of the polypeptide. The peptides, polypeptides, fusion polypeptides, compositions may also enhance the activity, specificity, and/or fidelity of other polypeptides in a reaction mixture. The disclosure also provides methods of using such peptides, polypeptides, fusion polypeptides, compositions.

Abstract: The present invention provides methods and compositions for treating bladder cancer. In particular, the present invention provides a fusion protein comprising a toxin moiety that is linked to an epithelial growth factor (EGF) moiety. The toxin moiety and the EGF moiety can be linked optionally via a linker. Typically, the fusion protein is administered intravesically into the cancerous bladder.

Abstract: Disclosed are methods and kits applicable to sequencing methods, such as Sanger dideoxy sequencing methods. The methods and kits disclosed utilize a cationically charged nucleic acid terminator in combination with a discriminatory polymerase.