Abstract: A real time Taq-Man PCR assay for detecting multiple serotypes of human papillomavirus (HPV) wherein the number of serotypes detected exceeds the number of colorimetric channels for detection. A biological sample is combined with three oligonucleotide primer/probe sets such that the probes and primers anneal to a target sequence. Each primer/probe set is at least preferential for a specific serotype of an organism. The first and second primer/probe sets are degenerate with respect to each other. The third primer/probe set is not degenerate with respect to the first and second primer/probe sets and discriminates for a third serotype. The third primer/probe set has a signal moiety that emits signal at a wavelength that is the same or different from the wavelength emitted by the signal moiety of the degenerate primer/probe set probes. The target sequences, if present, are amplified and detected.

Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Abstract: The invention describes composition and methods of use for novel hairpin blocked-cleavable primers. In one embodiment unblocking occurs through action of RNase H2. The method improves the specificity of PCR and reduces primer dimer events, enabling higher level multiplex reactions. Additionally, the invention protects RNA-containing primers from attack by single-strand RNases.

Abstract: The present invention provides a method of amplifying an RNA molecule in a biological sample by reverse transcription PCR (RT-PCR), wherein the RT-PCR is carried out in a solution comprising a) a polar aprotic solvent; b) a serum albumin; and optionally c) a non-ionic surfactant and/or a betaine.

Abstract: The invention relates to a high throughput method for determining telomere length of mammalian chromosomal DNA; primers for use in said method; a kit comprising said primers; use of said method to diagnose or prognose or to determine the risk of developing a telomere shortening disease such as cancer, ageing, neurological disorders including Alzheimer's disease, Parkinson's disease and other dementias, brain infarction, heart disease, chronic HIV infection, chronic hepatitis, skin diseases, chronic inflammatory bowel disease including ulcerative colitis, anaemia, atherosclerosis, Barrett's oesophagus and cancers including pre-cancerous conditions, infertility, telomere syndromes including dyskeratosis congenita, aplastic anaemia, idiopathic pulmonary fibrosis, familial myelodysplastic syndrome-acute myeloid leukaemia, Hoyeraal-Hreiderasson syndrome, Revesz syndrome, Coats plus syndrome, bone marrow failure, and cryptogenic liver cirrhosis.

Abstract: A method for quantifying individual mature tRNA species, comprising: incubating mature tRNA in a buffer to remove the amino acids from the 3? end; annealing a DNA/RNA stem-loop adapter; ligating the annealed hybrid stem-loop adapter to the mature tRNA; and amplifying and quantifying the ligation product by TaqMan qRT-PCR.

Abstract: Traditional enzyme characterization methods are low-throughput, and therefore limit engineering efforts in synthetic biology and biotechnology. Here we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein purification and by limiting the need for liquid chromatography mass spectrometry (LCMS) product detection by linking enzymatic function to DNA modification. DLEnCA is generalizable for many enzymatic reactions, and here we adapt it for glucosyltransferases, methyltransferases, and oxidoreductases. The assay utilizes cell free transcription/translation systems to produce enzymes of interest, while UDP-Glucose and T4-?-glucosyltransferase are used to modify DNA, which is detected post-reaction using qPCR or similar means of DNA analysis. For monitoring methyltransferases, consumption of SAM is observed by coupling to EcoRI methyltransferase.

Abstract: The present invention provides improved tests for the detection: of methicillin-resistant Staphylococcus aureus bearing a variant mecA gene. The tests are particularly useful for eliminating certain false negative results due to the presence of this variant in MRSA in patient samples.

Abstract: Method to perform a PCR assay that comprises the following steps: a. Obtaining a nucleic acid sample; b. Hybridizing that nucleic acid sample to one or more pair of primers where at least one primer consists of a single stranded DNA polynucleotide having a length of 60 or more nucleotides; c Subjecting said nucleic acid sample to a PCR, wherein the reaction mixture medium contains at least one of said primers; and d. Detecting the length of the amplified products. The amplified nucleic acid may contain any sequence or multiple sequences of STRs (short tandem repeats), genes or any coding region having a defined location on a genome. The preferred nucleic acid samples to be amplified are degraded or fragmented and contain one or more genetic markers.

Abstract: Kits and methods for detecting pathogens without the need for laboratory equipment are disclosed. The kits and methods described herein allow for near-room temperature amplification of pathogen polynucleotides in a biological sample in a one-compartment reaction vessel. The kits and methods may be used to detect any target nucleic acid, such as DNA or RNA from a bacterial, fungal, or viral pathogen.

Abstract: Methods of detecting the absence or presence of a micro-organism in a sample comprising: contacting the sample with a nucleic acid molecule which acts as a substrate for nucleic acid modifying activity of the micro-organism in the sample, incubating the thus contacted sample under conditions suitable for nucleic acid modifying activity; and specifically determining the absence or presence of a modified nucleic acid molecule resulting from the action of the nucleic acid modifying activity on the substrate nucleic acid molecule to indicate the absence or presence of the micro-organism. Corresponding kits are also provided.

Abstract: The invention relates to a method of identifying a specific yeast species in patient tissue or body fluid. The method comprises the steps of extracting and recovering DNA of the yeast species from the patient tissue or body fluid, amplifying the DNA, hybridizing a probe to the DNA to specifically identify the yeast species, and specifically identifying the yeast species. The invention also relates to a method of identifying a yeast mycotoxin in patient tissue or body fluid. The method comprises the steps of extracting and recovering the yeast mycotoxin from the patient tissue or body fluid, contacting the yeast mycotoxin with an antibody directed against the yeast mycotoxin, and identifying the yeast myocotoxin. Both of these methods can be used to determine if a patient is at risk for or has developed a disease state related to a yeast infection, and to develop an effective treatment regimen for the patient.

Abstract: Methods, polynucleotides, kits, and reaction mixtures are disclosed for the enriching of short polynucleotide molecules that have a length within a desired target length range. A Type IIS or Type III restriction enzyme is used to cleave polynucleotides at cleavage sites located at a distance from the restriction enzyme recognition sites. For example, a mixture of polynucleotides can be formed by inserting DNA molecules between a recognition site for the restriction enzyme and a region of non-naturally-occurring nucleotides that block cleavage by the restriction enzymes. If a polynucleotide contains a DNA molecule with a length within a target range, then the cleavage site will be within the blocking region, and cleavage will not occur. Polynucleotides containing DNA molecules with lengths outside the target range can be cleaved. By selectively enriching, through PCR or other means, polynucleotides that are intact, a concentrated population of polynucleotides of a target length can be formed.

Abstract: The disclosure provides methods, devices, and kits for conducting a quantitative analysis of a whole blood sample. Various modifications to the disclosed methods, devices, and kits are described.

Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Abstract: The present invention provides a method for analyzing a template nucleic acid, a method for analyzing a target substance, an analysis kit for a template nucleic acid or a target substance, and an analyzer for a template nucleic acid or a target substance, which are excellent in accuracy.

Abstract: Apparatus and methods to identify nucleotides of a DNA strand. The method includes exposing the DNA strand to a first dye or peptide, attaching the first dye or peptide to a first type of nucleotide (A,T,C,G) of the DNA strand, the first dye or peptide changing a conductance of the first type of nucleotide to which the first dye or peptide is attached, and measuring a tunneling current signal for all nucleotides of the DNA strand, the changed conductance of the first type of nucleotide providing amplified tunneling current discrimination of the nucleotides of the DNA strand.

Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.

Abstract: Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: A composition and method for controlled in vitro fragmentation of nucleic acids. A transposase forms catalytically active complexes with a modified transposon end that contains within its end sequence degenerate, apurinic/apyrimidinic sites, nicks, or nucleotide gaps, to fragment or shear a target nucleic acid sample in a controlled process. This method yields desired average nucleic acid fragment sizes. The inventive composition and method may be applied for generation of DNA fragments containing shortened transposon end sequences to facilitate subsequent reactions, for production of asymmetrically tailed DNA fragments, etc.