Abstract: Mismatch Repair Detection (MRD), a novel method for DNA-variation detection, utilizes bacteria to detect mismatches by a change in expression of a marker gene. DNA fragments to be screened for variation are cloned into two MRD plasmids, and bacteria are transformed with heteroduplexes of these constructs. Resulting colonies express the marker gene in the absence of a mismatch, and-lack expression in the presence of a mismatch. MRD is capable of detecting a single mismatch within 10 kb of DNA. In addition, MRD can analyze many fragments simultaneously, offering a powerful method for high-throughput genotyping and mutation detection.

Abstract: The present invention relates to methods and kits for detecting the presence or absence of a target DNA sequence, such as a mutation, within an identified region of a selected DNA molecule, such as a gene. In particular aspects, the invention relates to the use of certain aspects of the polymerase chain reaction (“PCR”) and ligase chain reaction (“LCR”) techniques for the detection of genetic mutations in genes, particularly point mutations. A kit has been developed for direct EPR detection of specific PCR amplified target nucleic acid sequences. The PCR reaction is carried out in the presence of nitroxide-labeled oligomers that are degraded only if hybridized to a complementary target sequence. The degradation of the nitroxide-labeled oligomers into nitroxide-labeled cleavage products results in a characteristic increase of the h-/ho ratio of the EPR signal; in the absence of a complementary target sequence the EPR signal of nitroxide-labeled oligomer remains unchanged.

Abstract: The method consists of detecting an enteric virus in a test sample, where the detection of said enteric virus in said test sample indicates the existence of contamination. The method allows us to detect the presence or absence of enteric viruses in a test sample, and then to determine the existence of environmental contamination, especially faecal contamination of livestock origin, in the test sample and, therefore, the place where the test sample was taken. The characterisation and/or molecular or serological typification of the enteric virus detected and its comparison with that of other enteric viruses present in sources of contamination near to where the samples were taken for analysis, also allows us to identify the origin of said contamination.

Abstract: Synthetic probes and methods for detecting analytes using such probes are described. The probes contain an analyte reactive moiety linked to a nucleic acid molecule that can be extended by DNA polymerase.

Abstract: Disclosed herein are nucleic acid sequences that encode novel polypeptides. Also disclosed are polypeptides encoded by these nucleic acid sequences, and antibodies, which immunospecifically-bind to the polypeptide, as well as derivatives, variants, mutants, or fragments of the aforementioned polypeptide, polynucleotide, or antibody. The invention further discloses therapeutic, diagnostic and research methods for diagnosis, treatment, and prevention of disorders involving any one of these novel human nucleic acids and proteins.

Abstract: Nucleic acid based methods for detecting the presence of E. coli or Shigella or related microorganisms in a sample using one or more E. coli or Shigella species specific nucleotide sequences are disclosed. More particularly the identification of molecules capable of binding or otherwise facilitating abnormal cell growth or abnormal physiology such as found in cancer or cellular instability is described. Further, molecular probes for performing the nucleic-acid based methods and methods of testing and selecting nucleic acid sequences suitable for same are provided. The methods and polynucleotides are useful inter alia in the testing of food and water samples, for testing for genetic and cellular instability, and for testing benign, pre-neoplastic and neoplastic disease in asymptomatic or symptomatic colorectal or gastric cancer patients or those at risk of the aforementioned conditions or those infected by Escherichieae and with other diseases or conditions.

Abstract: The present invention provides a polymorphic marker found in a region of the interferon receptor gene that can be used to assess the efficacy of interferon therapy. Thus, the present invention also relates to methods of assessing the efficacy of interferon therapy in an individual and means for accomplishing such a method.

Abstract: The present invention relates to reverse transcription of RNA, and in particular to reverse transcription by thermostable DNA polymerases. Thermoactinomyces vulgaris and Bacillus stearothermophilus possess reverse transcriptase activity in the presence of magnesium or manganese ions. Methods, compositions, and kits for reverse transcription and RT-PCR are also provided.

Abstract: Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

Abstract: The present invention describes methods of detecting a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a colorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer. Cleavage of the polyphosphate product of phosphoryl transfer via phosphatase leads to a detectable change in the label attached thereon. When the polymerase assay is performed in the presence of a phosphatase, there is provided a convenient method for real-time monitoring of DNA or RNA synthesis and detection of a target nucleic acid.

Abstract: Disclosed herein are isolated nucleic acid molecules that may be used as an internal positive controls in probe-based nucleic acid assays such as TaqMan® based assays. Also disclosed are probes comprising the isolated nucleic acid molecule of the present invention. The probes may comprise a reporter molecule and a quencher molecule. Also disclosed are assays which comprise using the probe of the present invention. The probes may be used to distinguish false negative results from true negative results in assays for a target nucleic acid molecule. The probe may be used in conjunction with probe-based nucleic acid assays for the detection of an organism such as one belonging to Bacillus, Mycobacterium, Francisella, Brucella, Clostridium, Yersinia, Variola, Orthopox, or Burkholderia.

Abstract: The present invention provides a method for the rapid simultaneous production of a plurality of single-stranded DNA circles having a predetermined size and nucleotide sequence using pre-designed hairpin oligonucleotides containing complementary sequences for directing ligation to form dumbbell-shaped monomers followed by heat denaturation to yield single-stranded DNA circles.

Abstract: Primers specific for races of pathogenic fungi which are resistant to certain fungicides are used in polymerase chain reaction assays for the detection of fungal pathogens. The use of these primers enables the detection of specific isolates of fungal pathogens and the monitoring of disease development in plant populations. The invention includes DNA sequences which show variability between different fungal pathotypes. Such DNA sequences are useful in the method of the invention as they can be used to derive primers for use in polymerase chain reaction (PCR)-based diagnostic assays. These primers generate unique fragments in PCR reactions in which the DNA template is provided by specific fungal pathotypes and can thus be used to identify the presence or absence of specific pathotypes in host plant material before the onset of disease symptoms.

Abstract: A method of characterizing a nucleic acid sample is provided that includes the steps of: (a) conducting a DNA polymerase reaction that includes the reaction of a template, a non-hydrolyzable primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and an enzyme having 3??5? exonuclease activity which reaction results in the production of labeled polyphosphate; (b) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species characteristic of the sample; (c) detecting the detectable species; and (d) characterizing the nucleic acid sample based on the detection.

Abstract: The present invention relates to a process for sensing biological or chemical changes in molecular structural shape or mass of molecules attached to the surface of a transverse shear piezoelectric oscillating molecular sensing device driven by a network analyzer. The process comprises the steps of i) exciting the sensor device at a series of predetermined frequencies, ii) collecting data to determine values for the predetermined parameters of series resonance frequency shift (fS), motional resistance (RM), motional inductance (LM), motional capacitance (CM), electrostatic capacitance (Co) and boundary layer slip parameter (?); and iii) determining relative changes in the measured parameters to detect thereby any changes in molecular structural shape or mass at sensing device surface.

Abstract: Novel polynucleotides isolated from Lactobacillus rhamnosus, as well as probes and primers, genetic constructs comprising the polynucleotides, biological materials, including plants, microorganisms and multicellular organisms incorporating the polynucleotides, polypeptides expressed by the polynucleotides, and methods for using the polynucleotides and polypeptides are disclosed.

Abstract: Fluorescent labels having at least one donor and at least one acceptor fluorophore bonded to a polymeric backbone in energy transfer relationship, as well as methods for their use, are provided. Of particular interest are the subject labels wherein the polymeric backbone is a nucleic acid and the donor fluorophore is bonded to the 5? terminus of said nucleic acid. Such labels find use as primers in applications involving nucleic acid chain extension, such as sequencing, PCR and the like.

Abstract: A method for the selection of one or more desired polypeptides includes cell free expression of nucleic acid molecules immobilized on a solid support system to produce polypeptides. The solid support carrying system is for biospecific interaction with at least the desired polypeptide or a molecule attached thereto. The method also includes separation of the solid support carrying both the desired polypeptide and the nucleic acid encoding it. Finally, the method optionally includes recovery of the nucleic acid and/or the desired polypeptide, and molecular libraries for use in these methods.

Abstract: The invention provides a new primer composition for detecting the presence of Shigella sonnei and a method of using the same. The primer composition and method have high specificity and sensitivity on the detection of Shigella sonnei.

Abstract: The invention provides a method that allows the construction of a chimeric and/or modified and/or reconstructed DNA molecule from two DNA fragments in a defined order and orientation, and to clone the molecule one step in a suitable vector using site specific recombination. No initial step of classical cloning via restriction enzymes is needed, in contrast to the classical recombination systems. This method allows the reliability of the recombination method for cloning with the flexibility of PCR to introduce modifications in the insert sequence. Moreover, this method allows the construction of chimerical DNA molecules associating two different elements, such as promoter-gene association or fusion proteins.