Abstract: Provided herein are methods to discover and use single nucleotide polymorphisms (SNP) for identifying breed, or line and breed, or line composition of a bovine subject. The present invention further provides specific nucleic acid sequences, SNPs, and SNP patterns that can be used for identifying breed or breed combinations for Angus, Holstein, Limousin, Brahman, Hereford, Simmental, Gelbvieh, Charolais and Beefmaster breeds. These patterns can be utilized to manage animals in a feedlot to obtain optimum performance based on known characteristics of specific breeds and identify animals for breeding in selection programs. In another aspect, these patterns can be used to ensure labeling on breed specific branded products.

Abstract: A screening method for identifying an individual having a pre-disposition towards having a cancer is disclosed, which screening method comprises the steps of: (a) obtaining a test sample comprising a nucleotide sequence comprised in the MYH gene of the individual or an amino acid sequence of a polypeptide expressed thereby; and (b) comparing a region of the test sample sequence with the corresponding region of the wild type sequence, whereby a difference between the test sample sequence and the wild type sequence signifies that the individual is pre-disposed to having the cancer; and wherein the difference comprises a specified variation.

Abstract: There are disclosed apparatus and methods for the field-assisted acceleration of biological processes involving charged entities, including in particular the detection of target DNA in a biological sample. A reaction cell is provided with a dielectric surface, and a field is generated by inducing charge-separation in the dielectric material by applying a potential to an electrode in contact with the dielectric material.

Abstract: A novel limited primer extension reaction improves detection sensitivity and specificity in a variety of hybridization platforms. In the invention, a sequence of target DNA that lacks one of the four types of nucleic acid bases for a span of eight or more adjacent nucleotide positions is selected for use. This sequence is referred to as the extension complement sequence, or ECS. A primer with a sequence that is complementary to the target sequence that is immediately downstream (to the 3? side) of this ECS is used to initiate an extension reaction. Extension occurs using a DNA polymerase and standard deoxynucleoside triphosphates for three of the four types of nucleic acid bases. The fourth base, which is complementary to the base missing in the ECS, is either absent or present only in the form of a dideoxynucleoside triphosphate, which does not support further extension. In either case, the extension reaction does not proceed past the first occurrence in the template of the base that is missing in the ECS.

Abstract: The present invention is directed to novel methods of synthesizing multiple copies of a target nucleic acid sequence which are autocatalytic (i.e., able to cycle automatically without the need to modify reaction conditions such as temperature, pH, or ionic strength and using the product of one cycle in the next one). In particular, the present invention discloses a method of nucleic acid amplification which is robust and efficient, while reducing the appearance of side-products. The method uses only one primer, the “priming oligonucleotide,” a promoter oligonucleotide modified to prevent polymerase extension from its 3?-terminus and, optionally, a means for terminating a primer extension reaction, to amplify RNA or DNA molecules in vitro, while reducing or substantially eliminating the formation of side-products. The method of the present invention minimizes or substantially eliminates the emergence of side-products, thus providing a high level of specificity.

Abstract: In a method for amplifying a DNA, comprising performing PCR using a sense primer and an antisense primer, PCR is performed in the presence of an additional sense primer comprising the sense primer and an oligodeoxyribonucleotide having a first additional sequence and ligated to the 5? end of the sense primer and an additional antisense primer comprising the antisense primer and an oligodeoxyribonucleotide having a second additional sequence complementary to the first additional sequence and ligated to the 5? end of the antisense primer; a Tm value of the additional sequences is lower than Tm values of the sense primer and the antisense primer; and annealing temperature in PCR is initially set to be a temperature at which the additional sequences do not anneal and changed in the course of PCR to a temperature at which the additional sequences anneal to each other.

Abstract: The present invention provides a combination of oligonucleotides preferable for composing a rapid and specific gene testing reagent for Shiga toxin family gene type 2 (stx) of entero-hemorrhagic Escherichia coli (EHEC). More specifically, the present invention provides a method for detecting stx2 RNA of EHEC by specifically amplifying only stx2 RNA using a primer having a sequence homologous or complementary to a base sequence specific for stx2 gene of EHEC and located at sites free of alterations between genotypes, and an oligonucleotide that binds to a specific site of stx2 RNA.

Abstract: Methods and kits are provided for non-preferential amplification of a population of nucleic acids. The methods allow for a high degree of amplification, where representation in the final population has a direct linear relationship with the starting material. The amplification product is useful as a probe for hybridization; for generation of libraries, for sequencing, and the like.

Abstract: Mutant RNA polymerases of phagic origin in which the peptide chain is modified by substitution, deletion or addition of at least one amino acid, the modification having the effect of reducing the sensitivity of the RNA polymerases to the initial transcription sequence of the DNA sequence coding for the RNA, for a method for production of the RNA, or proteins coded by the RNA, from given nucleotide sequences, comprising a sequence of DNA coding for the RNA, the transcription of which is placed under the control of a promoter recognised by wild-type RNA polymerases and the mutant RNA polymerases as above. The method has a higher yield of RNA than the yield obtained when using the wild-type RNA polymerases in the presence of the same non-consensual ITS as that found in the sequence of DNA coding for the RNA.

Abstract: The first primer of the invention is a primer which, when used in PCR under appropriate conditions, serves to detectably amplify 16S rRNA-encoding DNAs of bacteria of the Escherichia, Salmonella and Vibrio genera, but when used in PCR under the same conditions, does not serve to detectably amplify either chloroplast 16S rRNA-encoding DNAs or mitochondrial 16S rRNA-encoding DNAs. The second primer of the invention is a primer which, when used in PCR under appropriate conditions, serves to detectably amplify 16S rRNA-encoding DNAs of Staphylococcus aureus and Bacillus cereus, but when used in PCR under the same conditions, does not serve to detectably amplify either chloroplast 16S rRNA-encoding DNAs or mitochondrial 16S rRNA-encoding DNAs.

Abstract: A nucleic acid amplification method, and probes for use within the method are described.

Abstract: This invention relates to a method for efficiently detecting double-stranded nucleic acids. More particularly, this invention relates to a method for reducing signals derived from an intercalator bound to a single-stranded nucleic acid, wherein a compound that reacts more preferentially with an intercalator bound to a single-stranded nucleic acid than with an intercalator bound to a double-stranded nucleic acid or a compound that is bound to a single-stranded nucleic acid more strongly than an intercalator and is bound to a double-stranded nucleic acid more weakly than an intercalator is added to a mixture comprising double-stranded and single-stranded nucleic acids both having intercalators bound thereto, thereby reducing signals derived from an intercalator bound to a single-stranded nucleic acid.

Abstract: The present invention relates to a method for identifying individuals with Parkinson's disease and/or individuals at risk for developing Parkinson's disease, comprising screening nucleic acids from the individual for a mutation in the ADH1C gene, as well as different uses thereof.

Abstract: The present invention provides methods and kits useful for detecting neplasia by measuring the methylation level of biomarkers, especially the promoter region of GSTP1 for the detection of prostate adenocarcinoma.

Abstract: This invention relates to methods of sequencing DNA. More specifically, this invention relates to methods of sequencing both the sense and antisense strands of DNA through the use of blocked and unblocked sequencing primers. In brief, these methods include the steps of annealing an unblocked primer to a first strand of nucleic acid; annealing a second blocked primer to a second strand of nucleic acid; elongating the nucleic acid along the first strand with a polymerase; terminating the first sequencing primer; deblocking the second primer; and elongating the nucleic acid along the second strand.

Abstract: A method for preparing an antigen-specific antibody by constructing a library of phage-displayed single chain variable fragment of an antibody with a novel frame-shifting PCR is disclosed. Also disclosed is a method for preparing a clone for producing an antigen-specific antibody.

Abstract: The invention provides methods for sequencing a nucleic acid comprising stabilizing a primer/target nucleic acid duplex on a substrate. Methods of the invention generally contemplate the use of a dual-anchored primer/target nucleic acid duplex, or a stabilizing molecule in a single molecule sequencing reaction.

Abstract: The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.

Abstract: The invention relates to a method for the isolation of hepatitis C virus. The method comprises the separation of particles termed exosomes from the blood plasma of an individual infected with hepatitis C virus (HCV) and the extraction or RNA from these exosome particles.

Abstract: The invention provides methods and compositions for the amplification and replication of nucleic acid molecules. In particular, novel amplification methods, referred to herein as polynomial amplification, are provided. According to these methods, a nucleic acid molecule to be amplified is contacted with at least two primers; a non-replicable primer which may hybridize to the nucleic acid molecule being amplified, and a replicable primer which may hybridize to a primer extension product generated from extension of the non-replicable primer.