Abstract: The GADD153 gene is used herein as a molecular marker for in vivo tumor cell injury which occurs in response to chemotherapy. A GADD153-based prognostic method for tumor clinical response in a patient undergoing chemotherapy is provided. By determination of the magnitude of increase, above baseline, in GADD153 mRNA in a sample derived from a tumor in a patient after administration of a chemotherapeutic agent, the method is able to predict the tumor clinical response and, thus, the patient therapeutic response. This method is advantageous over known prognostic methods for tumor clinical response in that it can accurately and rapidly predict therapeutic responses including tumor progression, partial regression and complete regression for a wide range of tumors and chemotherapeutic agents.

Abstract: Genetic polymorphisms are identified in the human CYP3A4 gene that alter CYP3A4-dependent drug metabolism. Nucleic acids comprising the polymorphic sequences are used to screen patients for altered metabolism for CYP3A4 substrates, potential drug-drug interactions, and adverse/side effects, as well as diseases that result from environmental or occupational exposure to toxins. The nucleic acids are used to establish animal, cell and in vitro models for drug metabolism.

Abstract: A PCR-based method for the identification of species of the genus Eimeria, (commonly known as coccidia), is described. The method is genus-specific and utilizes either, or both, of two novel primer sets; designated WW1 (SEQ ID NO:31) and WW3r (SEQ ID NO:32), and, WW2 (SEQ ID NO:33) and WW4r (SEQ ID NO:34).

Abstract: Compositions and methods for detecting the conversion to mucoidy in Pseudomonas aeruginosa are disclosed. Chronic respiratory infections with mucoid Pseudomonas aeruginosa are the leading cause of high mortality and morbidity in cystic fibrosis. The initially colonizing strains are nonmucoid but in the cystic fibrosis lung they invariably convert into the mucoid form causing further disease deterioration and poor prognosis. Mucoidy is a critical P. aeruginosa virulence factor in cystic fibrosis that has been associated with biofilm develoment and resistance to phagocytosis. The molecular basis of this conversion to mucoidy is also disclosed. The present invention provides for detecting the switch from nonmucoid to mucoid state as caused by either frameshift deletions and duplications or nonsense changes in the second gene of the cluster, mucA. Inactivation of mucA results in constitutive expression of genes, such as algD, dependent on algU for transcription.

Abstract: The present invention provides methods for the identification of nucleic acid molecules corresponding to genes regulated by a transcription factor comprising: cross-linking a transcription factor to a nucleic acid molecule in a cell forming a transcription factor-nucleic acid molecule complex; fragmenting the nucleic acid molecule to form a transcription factor-nucleic acid molecule fragment complex; isolating the nucleic acid molecule fragment; combining the isolated nucleic acid molecule fragment with a cDNA library of sequences known to be complementary to previously identified nucleic acid molecules, or a cDNA obtained by reverse transcription of a population of RNA molecules, to form a mixture comprising an isolated nucleic acid molecule fragment-cDNA complex; amplifying the cDNA in the isolated nucleic acid fragment-cDNA complex using the nucleic acid molecule fragment as a primer; and identifying the amplified cDNA molecule by sequencing the cDNA molecule and comparing to known sequences or hybridizati

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the enzyme peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the enzyme peptides, and methods of identifying modulators of the enzyme peptides.

Abstract: Polynucleotide probes and accessory helper oligonucleotides useful for detecting bacteria that are members of the genus Staphylococcus. The hybridization probes are highly specific for Staphylococcal bacteria and do not cross-hybridize with the rRNA or rDNA of numerous other bacterial and fungal species.

Abstract: This invention provides novel methods for assessing HPV infection. Gene expression levels are used to assess the progression of HPV infection from benign to malignant growth. Also provided are kits for carrying out the methods of this invention.

Abstract: A method for separating microorganisms, especially infectious agents, from a mixture by two dimensional centrifugation on the basis of sedimentation rate and isopycnic banding density, for sedimenting such microorganisms through zones of immobilized reagents to which they are resistant, for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes. The method is based on the discovery that individual microorganisms, such as bacterial and viral species, are each physically relatively homogeneous, and are distinguishable in their biophysical properties from other biological particles, and from non-biological particles found in nature.

Abstract: A method for predicting the constitution susceptible to the onset of specific diseases in individual humans, for example, respiratory diseases such as chronic obstructive pulmonary diseases, sinobronchial syndrome, pulmonary emphysema, diffuse panbronchiolitis or bronchiectasis, effects of treatment on patients or prognosis of the treatment by analyzing the genetic polymorphisms of a human trypsin-like enzyme of the respiratory tract.

Abstract: Isolated polynucleotide molecules and peptides encoded by these molecules are used in the analysis of human carbamyl phosphate synthetase I phenotypes, as well as in diagnostic and therapeutic applications, relating to a human carbamyl phosphate synthetase I polymorphism. By analyzing genomic DNA or amplified genomic DNA, or amplified cDNA derived from mRNA, it is possible to type a human carbamyl phosphate synthetase I with regard to the human carbamyl phosphate synthetase I polymorphism, for example, in the context of diagnosing and treating hepatic veno-occlusive disease (HVOD) associated with bone marrow transplants.

Abstract: This invention provides sensitive nucleic acid hybridization assay methods for the detection of target human nucleic acids in a biological sample, such as acellular fluids. The methods are particularly useful in early diagnosis of chronic illnesses.

Abstract: A method of analyzing a sequence of a polynucleotide of interest, comprising the steps of: a) incorporating one member of a specific binding pair at the end of each strand of a double stranded polynucleotide of interest, the number being of the same type for both strands, b) immobilizing both strands of the polynucleotide to a solid support provided with the other member of the specific binding pair, c) annealing sequencing primers to the immobilized strands, d) sequencing both strands by the chain termination method. The polynucleotide of interest is preferably amplified before or in connection with step a) and most preferably by polymerase chain reaction extension. The invention also comprises a kit for use in analyzing the sequence of a polynucleotide of interest.

Abstract: A method for detecting mutations, such as a single base change or an addition or deletion of about one to four base pairs, is based on the use of an immobilized DNA mismatch-binding protein, such as MutS, which binds to a nucleic acid hybrid having a single base mismatch or unpaired base or bases, thereby allowing the detection of mutations involving as little as one base change in a nucleotide sequence. Such a method is useful for diagnosing a variety of important disease states or susceptibilities, including the presence of a mutated oncogene and the presence of DNA containing triplet repeat sequences which characterize several genetic diseases including fragile X syndrome. The present method is used to isolate or remove by affinity chromatography duplex DNA molecules containing mismatches such as error-containing molecules in PCR-amplified DNA samples. Methods for detecting and enriching minority sequences are disclosed.

Abstract: Purified DNA including a sequence encoding Diabetogene rad.

Abstract: The present invention provides the use of animal calculus as a source of nucleic acid which is useful in genetic studies. Such genetic studies may center on the host organism from which the calculus is derived or on microbial organisms whose nucleic acid is embedded in the calculus of the animal host.

Abstract: A solid medium for storage of DNA, including blood DNA, comprising a solid matrix having a compound or composition which protects against degradation of DNA incorporated into or absorbed on the matrix. Methods for storage of DNA using this solid medium, and for recovery of DNA or in situ use of DNA are also disclosed.

Abstract: The present invention relates to the simultaneous and specific identification of the variant forms of &agr;-thalassemia. This invention utilizes simple and readily available equipment to rapidly identify, diagnose and differentiate the different forms of &agr;-thalassemia. Specifically, the present invention relates to a simple and rapid non-radioisotopic technique for the diagnosis and differentiation of the common forms of &agr;-thalassemia has been developed. This approach works on any biological tissue including blood, wherein the assay works equally well with fresh blood and dried blood samples stored on filter paper.

Abstract: The invention provides a method for determining whether a test compound binds to a target RNA, the method comprising the steps of: (a) contacting the test compound with a pair of indicator molecules comprising an antimicrobial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair being capable of binding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer and/or quenching to take place; and (b) measuring the fluorescence of the target RNA and/or the antimicrobial in the presence of the test compound and comparing this value to the fluorescence of a standard.

Abstract: Methods for characterizing patients diagnosed with histaminergic diseases are described. Nucleic acid molecules that include a histamine-N-methyltransferase intron variant sequence associated with a histaminergic disease also are described.