Abstract: Methods and compositions for identifying novel pesticidal gene homologues are provided. Specifically, the methods of the invention comprise systematically designing oligonucleotide primers that are specific for a pesticidal gene of interest and performing successive rounds of PCR amplification of nucleic acid material from a microorganism, particularly a Bacillus thuringiensis strain, to identify novel homologues of known pesticidal genes. Oligonucleotide primers that can be used to practice the present methods are further disclosed.

Abstract: The invention provides methods and compositions for rapid, sensitive, and highly specific nucleic acid-based detection of B. anthracis in a sample. In general, the methods involve detecting within the sspE gene of B. anthracis the presence of a fragment of six unique contiguous nucleotides that is not present in the sspE genes of other Bacillus bacteria or other non-Bacillus bacteria. In many embodiments, the methods involve amplifying a nucleic acid comprising at least a fragment of an sspE gene from a sample, and detecting the presence of the six unique contiguous nucleotide fragments in the nucleic acid. The invention also provides primers and kits for detection of B. anthracis in a sample. The subject invention finds use in a variety of different applications, including research, medical, diagnostic and military applications.

Abstract: Provided is a method of treating a surface of a substrate used in a biochemical reaction system, the method including forming a polymer film on the surface by vapor deposition of a compound of formula (1) below and a compound of formula (2) below: (RO)3—Si—(CH2)n1—X ??(1) (RO)3—Si—(CH2)n2—(CF2)m—X ??(2) wherein R is one of a methyl group and an ethyl group, X is one of a methyl group and a trifluoromethyl group, n1 is an integer from 1 to 3, n2 is an integer from 1 to 10, and m is an integer from 1 to 10.

Abstract: A comprehensive set of human specific, target specific, multiplex PCR assays for DNA quantitation is provided. Our duplex qPCR for nDNA/mtDNA had a linear quantitation range of 100 ng to 1 pg, and our triplex qPCR assay for nDNA/mtDNA/male Y DNA had a linear range of 100 ng to 0.1 ng. Human-specificity was demonstrated by the accurate detection of 0.05% and 5% human DNA, respectively, from a complex source of starting templates. Target-specificity was confirmed by the lack of cross-amplification among targets. A high throughput alternative for human gender determination was also developed by multiplexing the male Y primer/probe set with an X chromosome based system. Background cross-amplification with DNA templates derived from fourteen other species was negligible aside from the male Y assay which produced spurious amplifications from other non-human primate templates. Mainstream application of these assays will undoubtedly benefit forensic genomics.

Abstract: Among the different intrastrand quadruplex structures that can arise from duplex DNA, it has been discovered that the nucleotide sequences (GGA)4 (SEQ ID NO: 1) and (GGA)3GG (SEQ ID NO: 2) form biologically significant quadruplex structures. Thus, provided herein are methods for identifying molecules that modulate the biological activity of quadruplex DNA comprising the nucleotide sequence (GGA)4 (SEQ ID NO: 1) or the nucleotide sequence (GGA)3GG (SEQ ID NO: 2), and specifically, methods for identifying molecules that bind such quadruplexes. Also provided herein are methods for modulating the biological activity of a biologically significant native quadruplex DNA with a molecule identified by the methods described herein.

Abstract: The inventions provides a method for identifying a target virus in an infected subject comprising the steps of designing a pair of degenerate primers corresponding to highly conserved regions of the target virus; designing a pair of species-specific primers according to highly variable sequences within the conserved regions of the target virus; preparing the species-specific probes according to the larger sequence variations within the conserved regions of the target virus, which are amplified with the species-specific primers as obtained; preparing a test sample by amplifying total nucleic acid of the infected subject with the degenerate primers as obtained; contacting the test sample with the species-specific probes as obtained; and detecting a hybridization between the species-specific probe and the test sample, wherein the hybridization indicates the target virus is identified in the infected subject. The primers and probes for detecting a garget virus are also provided.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

Abstract: A method for identifying an RNA form of a bacteria, comprising reverse transcribing RNA material; conducting PCR using primers for a first highly conserved genetic sequence generic of the bacteria; conducting nested PCR using primers for a second highly conserved genetic sequence within the first genetic sequence of the bacteria; and identifying the bacteria based on unconserved amplified sequences linked to the conserved sequences.

Abstract: The present invention provides amplification and hybridisation method for detecting and typing human papillomavirus (HPV), and the primers and hybridisation probes used in the method. The invention relates to a concrete part of the HPV genome, which is suitable for designing HPV genus-specific and HPV genotype-specific hybridisation oligonucleotide probes.

Abstract: Allele specific primers and probes suitable for detecting allelic variants of human SP-A2 gene for applications such as molecular diagnosis, prediction of an individual's susceptibility, and/or the genetic analysis of SP-A2 gene in a population.

Abstract: A mammalian KIR 4.1 gene and gene products which are predictive of a susceptibility or predisposition to neurological disorders such as multiple epilepsy phenotypes are provided. Methods of predicting an individual's susceptibility in developing or having a neurological disorder via detection of these diagnostic markers are also provided. In addition, compositions and methods for identifying compositions for use in the treatment of neurological disorders via these genes and gene products are described.

Abstract: The methods and apparatus disclosed herein concern nucleic acid sequencing by enhanced Raman spectroscopy. In certain embodiments of the invention, nucleotides are covalently attached to Raman labels before incorporation into a nucleic acid. In other embodiments, unlabeled nucleic acids are used. Exonuclease treatment of the nucleic acid results in the release of labeled or unlabeled nucleotides that are detected by Raman spectroscopy. In alternative embodiments of the invention, nucleotides released from a nucleic acid by exonuclease treatment are covalently cross-linked to nanoparticles and detected by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS). Other embodiments of the invention concern apparatus for nucleic acid sequencing.

Abstract: The invention provides isolated nucleic acid sequences encoding polypeptides having nucleoside phosphoramidase activity, and methods of screening for nucleoside phosphoramidate compounds that are cleaved by a phosphoramidase or for phosphoramidases that are able to cleave phosphoramidate compounds. The invention also provides methods of delivering a nucleoside monophosphate.

Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

Abstract: A primer set used to screen a polynucleotide sample to detect and identify variants in the Cytochrome P450 isoenzyme 2D6 (CYP2D6) gene. A method of screening a polynucleotide sample to detect and identify the presence of one or more than one variant in the CYP2D6 gene in the sample. A method of predicting the potential for altered metabolism of a substance, including one or more than one pharmaceutical drug, by a first individual compared to a second control individual, where the substance is metabolized by the CYP2D6 isoenzyme, and where the second control individual is homozygous for the wild type allele of the CYP2D6*1, SEQ ID NO:1. A method of screening a population to detect and identify the presence of one or more than one variant in the CYP2D6 gene. A purified or isolated variant of SEQ ID NO:1. A purified or isolated variant of SEQ ID NO:3.

Abstract: A method of determining the length of a particular region within a nucleic acid, the method comprising a) subjecting a sample of the nucleic acid to a plurality of amplification reactions in which the region is amplified, wherein the time of the extension phase in each of the reactions is varied; b) monitoring the progress of the amplification reactions; c) determining the minimum time during which extension phase of the amplification is completed within each reaction mixture and relating that to the length of the sequence undergoing extension. The method, combined with melting point analysis, will allow percentage GC content of a sequence to be determined. Length analysis of this type can be used in diagnosis or analysis as well as in recombinant DNA technology to check for the presence of concatamers, and in taxonomic classification or forensics. Apparatus for use in the method is also described and claimed.

Abstract: In one aspect, the present invention provides methods for synthesizing multiple copies of antisense cDNA molecules from an RNA molecule, comprising using an RNA molecule as a template for synthesizing multiple copies of antisense cDNA molecules. In some embodiments of the methods, the RNA molecule is incubated with a primer and with an enzyme possessing reverse transcriptase activity under suitable conditions for synthesizing multiple copies of antisense cDNA molecules. In some embodiments, the methods produce multiple copies of double-stranded cDNA from a template RNA molecule. In further embodiments, the methods produce multiple copies of cRNA from a template RNA molecule.

Abstract: The present invention provides methods for diagnosing mycobacteria other than tuberculosis (MOTT) infections in patients comprising amplifying the internal transcribed spacer sequence (ITSS) of 16S-23S rDNA of MOTT with primers that amplify MOTT but not Mycobacteria Tuberculosis (MTB). The present invention also provides a method for differentiating between MOTT and MTB infections comprising amplifying MOTT with primers that amplify MOTT but not MTB; amplifying MTB with primers that amplify MTB but not MOTT; and detecting approximately 130 base pair product indicative of MOTT and approximately 180 base pair product indicative of MTB.

Abstract: An isolated and purified nucleic acid comprising a gene specifically expressed in hop lupulin glands. Hops are dioecious, and only female plants bear cones, the lupulin glands of which contain secondary metabolic products which provide bitterness and flavor to beer. These secondary metabolic products contain some pharmacologically effective compounds. In order to breed a more useful cultivar of hops by manipulating the constituent of such useful secondary metabolic products relying on genetic engineering techniques, this invention provides an isolated and purified nucleic acid comprising a gene specifically expressed in hop lupulin glands. By using this nucleic acid, it is possible to develop a novel method for breeding hops with transformation techniques and molecular selection techniques. Furthermore, the present invention also provides a nucleic acid comprising the regulatory region for specifically expressing genes in lupulin glands. This nucleic acid can be used also for hop breeding.