Abstract: The present invention relates to a novel process for the preparation, by fermentation, of compounds of the formula I ##STR1## where R.sup.1 is hydrogen, fluorine, chlorine or bromine.

Abstract: A new species of Syngliocladium, designated as S. tetanopsis Hodge, Humber and Wozniak, has been discovered which is pathogenic to the sugarbeet root maggot, Tetanops myopaeformis Roder. Spore formulations of this entomopathogen are useful for inciting a fatal mycoses in the sugarbeet root maggot. This species represents the only confirmed natural pathogen of this dipteran insect.

Abstract: The present invention relates to a DNA-based computer which is able to perm mathematical calculations such as addition as well as logical operations. It is based, at least in part, on the discovery that DNA molecules can be used to perform operations analogous to "bit-flipping" in computers. This capability, referred to herein as "molecular bit-flipping", derives from the complementary nature of DNA sequences. According to the present invention, input data are each represented by single-stranded DNA molecules. Complementary DNA sequences are incorporated such that input molecules, which bear a relationship defined by the operation, hybridize and permit one or more template DNA strands to serve as templates for primer extension. Primer extension, in turn, creates a result DNA molecule which represents the output data, and may be read using straightforward molecular biological techniques.

Abstract: Disclosed are in situ hybridization methods for differentially detecting an RNA and the gene from which it was transcribed, while preserving the spatial relationship of the RNA transcript and the gene. Also disclosed are in situ hybridization methods for simultaneously detecting two alleles of the same gene in a single cell, while differentially detecting RNA transcribed each of the two alleles. Also disclosed are in situ hybridization methods for detecting normal and defective RNA splicing.

Abstract: Compositions and methods for the treatment and diagnosis of diseases or disorders amenable to treatment through modulation of expression of a nucleic acid encoding a platelet endothelial cell adhesion molecule-1 (PECAM-1; also known as CD31 antigen or endoCAM) protein are provided.

Abstract: The invention provides oligonucleotides containing methyl phosphotriester linkages and processes for making and methods for using such oligonucleotides.

Abstract: The invention involves methods and kits useful in determining specific mRNA molecules. The methods can be carried in a single reaction vessel, in that both reverse transcriptase and amplification can be carried out in the same, heat stable reaction vessel.

Abstract: A method is provided for determining the identity of a nucleotide at a preselected site in a nucleic acid molecule. The method involves the incorporation of a nucleoside triphosphate that is complementary to the nucleotide present at the preselected site onto the terminus of a primer molecule, and their subsequent ligation to a second oligonucleotide. The reaction is monitored by detecting a specific label attached to the reaction's solid phase or by detection in solution.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of G-alpha-11. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding G-alpha-11. Methods of using these compounds for modulation of G-alpha-1l expression and for treatment of diseases associated with expression of G-alpha-11 are provided.

Abstract: The present invention provides methods for preparing a stool sample in order to screen for the presence of indicators of a disease, for example a subpopulation of cancerous or precancerous cells. The methods take advantage of the recognition that cellular debris from cancerous and precancerous cells is deposited onto only a longitudinal stripe of stool as the stool is forming in the colon. Accordingly, methods of the invention comprise obtaining a representative sample, such as a circumferential or cross-sectional sample of stool in order to ensure that any disease indicator, such as cellular debris that is shed by colonic cells, is obtained in the sample.

Abstract: Reporter-quencher probe assays of nucleic acid amplification, such as PCR, are rendered more meaningful by the addition of internal control reagents. An internal control polynucleotide is amplified with internal control primers and the product is measured by correlation with increased fluorescence by polymerase mediated-exonuclease cleavage or hybridization of the internal control probe. Probes specific for target and internal control polynucleotides are labelled with spectrally resolvable reporters, allowing for concurrent detection and measurement of target and control amplification. A kit of all PCR reagents can be dispensed into reaction chambers in a high-throughput system for rapid and accurate nucleic acid amplification assay, with real-time or end-point measurements. Fluorescent signals correlated to target and internal control levels are spectrally resolvable and measured concurrently.

Abstract: This invention is a method for identifying hop varieties based on polymorphism in genetic sequences of hop varieties. Specifically, polymorphic regions of hop DNA are amplified by performing a polymerase chain reaction using an identifying primer designed to amplify regions comprising polymorphism in the base sequences of different varieties, and the amplified DNA fragments are analyzed. In this way, hop varieties can simply and accurately identified.

Abstract: The invention provides a human zygin-1 (ZY-1H) and polynucleotides which identify and encode ZY-1H. The invention also provides expression vectors, host cells, agonists, antibodies and antagonists. The invention also provides methods for treating disorders associated with expression of ZY-1H.

Abstract: The invention relates to a substantially pure thermostable DNA polymerase from Thermotoga (Tne and Tma) and mutants thereof. The Tne DNA polymerase has a molecular weight of about 100 kilodaltons and is more thermostable than Taq DNA polymerase. The mutant DNA polymerase has at least one mutation selected from the group consisting of (1) a first mutation that substantially reduces or eliminates 3'.fwdarw.5' exonuclease activity of said DNA polymerase; (2) a second mutation that substantially reduces or eliminates 5'.increment.3' exonuclease activity of said DNA polymerase; (3) a third mutation in the O helix of said DNA polymerase resulting in said DNA polymerase becoming non-discriminating against dideoxynucleotides. The present invention also relates to the cloning and expression of the wild type or mutant DNA polymerases in E. coli, to DNA molecules containing the cloned gene, and to host cells which express said genes.

Abstract: A DNA amplification and homogeneous DNA probe assay device is provided which includes a multiplicity of discrete sample cells in a flat "card" format, with each sample cell containing the reagents necessary for both DNA amplification and homogeneous DNA probe assay. The device is particularly suitable for fluorescence polarization DNA probe assays, aid is preferably provided with and integal polarizer to avoid the need for polarizing elements in the related measuring apparatus. The size and geometry of the sample cells allows for a "hot start" of the DNA amplification reaction and thereby avoids mis-priming of the amplification reaction.

Abstract: The invention relates to methods for targeting an exogenous polynucleotide or exogenous complementary polynucleotide pair to a predetermined endogenous DNA target sequence in a target cell by homologous pairing, particularly for altering an endogenous DNA sequence, such as a chromosomal DNA sequence, typically by targeted homologous recombination. In certain embodiments, the invention relates to methods for targeting an exogenous polynucleotide having a linked chemical substituent to a predetermined endogenous DNA sequence in a metabolically active target cell, generating a DNA sequence-specific targeting of one or more chemical substituents in an intact nucleus of a metabolically active target cell, generally for purposes of altering a predetermined endogenous DNA sequence in the cell.

Abstract: A method of regulating cholesterol related genes, enzymes and other compounds, pharmaceutical compositions and a kit related thereto are provided. Exemplary genes that are regulated include a gene for an LDL receptor, a gene for HMG-CoA reductase, a gene for cholesterol 7-alpha-hydroxylase, and a gene regulating a function involved in cholesterol homeostasis. The method comprises the step of parenterally administering a therapeutically effective amount of a lipid acceptor. The lipid acceptor in one variant includes a multiplicity of large liposomes comprised of phospholipids substantially free of sterol during a treatment period. The method includes the steps of periodically assaying plasma LDL concentrations with an assay during a period of time to assess the plasma LDL and to obtain an LDL profile, and adjusting the parenteral administration in response to the LDL profile.

Abstract: Oligonucleotides are provided which are targeted to nucleic acids encoding human serine/threonine protein phosphatases and which are capable of inhibiting protein phosphatase expression. Methods of inhibiting the expression of human protein serine/threonine phosphatases using oligonucleotides of the invention are also provided. The present invention further comprises methods of preventing or inhibiting hyperproliferation of cells and methods of treating abnormal conditions, including cancer, using oligonucleotides of the invention.

Abstract: This invention relates to agents and conjugates that can be used to detect and isolate target components from complex mixtures such as nucleic acids from biological samples, cells from bodily fluids, and nascent proteins from translation reactions. Agents comprise a detectable moiety bound to a photoreactive moiety. Conjugates comprise agents coupled to substrates by covalent bounds which can be selectively cleaved with the administration of electromagnetic radiation. Targets substances labeled with detectable molecules can be easily identified and separated from a heterologous mixture of substances. Exposure of the conjugate to radiation releases the target in a functional form and completely unaltered. Using photocleavable molecular precursors as the conjugates, label can be incorporated into macromolecules, the nascent macromolecules isolated and the label completely removed.

Abstract: Compositions and methods are provided for modulating the expression of protein kinase C. Oligonucleotides are provided which are targeted to nucleic acids encoding PKC. The oligonucleotides contain a methoxyethoxy (--O--CH.sub.2 CH.sub.2 OCH.sub.3) modification at the 2' position of at least one nucleotide. Methods of inhibiting PKC expression and methods of treating conditions associated with expression of PKC using oligonucleotides of the invention are disclosed.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of ELK-1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding ELK-1. Methods of using these compounds for modulation of ELK-1 expression and for treatment of diseases associated with expression of ELK-1 are provided.

Abstract: A nucleoside/tide compound having the structureNUC--L--S--LB/LGis described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure ##STR1## wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nuclcoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.

Abstract: A nucleic acid-bondable magnetic carrier of the present invention is a magnetic silica particle comprising a superparamagnetic metal oxide, wherein the magnetic silica particle has a specific surface of about 100 to about 800 m.sup.2 /g.

Abstract: The present invention relates to the discovery of a novel Hantavirus. In particular, the present invention relates to nucleic acids of the newly discovered virus and to nucleic acid reagents and antibodies for use in methods of detection and prevention of infection by the virus.

Abstract: Sequencing methods and methods for synthesizing DNA probes using mutant bacteriophage T4 DNA polymerases which have increased ability to incorporate modified nucleotides for the synthesis of long or short chains of complementary, modified, e.g., fluorophore-labeled DNA. In general, the mutant T4 DNA polymerases retain 3'.fwdarw.5' exonuclease activity; hence, reduction or elimination of 3'.fwdarw.5' exonuclease activity is not a prerequisite for efficient synthesis of a complementary fluorophore-labeled or other modified DNA. In fact, retention of 3'.fwdarw.5' exonuclease activity increases accuracy of DNA replication, because these exonucleases proofread or edit the product of DNA replication.

Abstract: Novel compounds isolated from the fermentation of producing cultures of Nodulisporium sp. are antiparasitic and insecticidal agents.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of RhoA. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding RhoA. Methods of using these compounds for modulation of RhoA expression and for treatment of diseases associated with expression of RhoA are provided.

Abstract: New hybrid ribozymes that exhibit the high metabolic stability of small nucleolar ribonucleic acids (snoRNAs), and that cleave target sequences with high efficiencies in either cis (intra-molecular) or trans (inter-molecular) configuration are described. The hybrid ribozymes include (i) a ribozyme catalytic sequence; and (ii) a snoRNA stabilizing motif; wherein the catalytic sequence and the stabilizing motif are arranged to provide the RNA molecule with a three-dimensional configuration in which the catalytic sequence is positioned to interact with a target sequence and the stabilizing motif adopts a conformation that stabilizes the RNA molecule, and additionally enables the RNA molecule to localize in the nucleolus of a cell.

Abstract: A novel, differential association between allele 2 of the variable number of tandem repeats polymorphism at intron 2 of the human IL-1 receptor antagonist gene and ulcerative colitis in humans of Jewish ancestry has been discovered. In accordance with the present invention, there is provided methods of screening for ulcerative colitis in human subjects of Jewish ancestry comprising detecting the presence or absence of nucleic acid of the subject encoding allele 2 of the variable number of tandem repeats polymorphism at intron 2 of the human IL-1 receptor antagonist gene, wherein the presence of nucleic acid encoding allele 2 is indicative of ulcerative colitis. Kits useful for screening for ulcerative colitis in human subjects of Jewish ancestry are also provided.

Abstract: The present invention provides for a method for generating a directed, recombinant fusion nucleic acid molecule which includes: (A) contacting a first pair of single-stranded primers with a first strand and a second strand of a first nucleic acid molecule and a second pair of single-stranded primers with a first strand and a second strand of a second nucleic acid molecule under hybridization conditions, (B) amplifying the first nucleic acid molecule and the first pair of primers and the second nucleic acid molecule and the second pair of primers under amplification conditions, separately; (C) mixing the amplification products from step (B) and the first primer of the first pair of primers and the second primer of the second pair of primers under hybridization conditions; (D) amplifying the hybridized molecules of step (C) under amplification conditions so as to generate a directed, recombinant fusion nucleic acid molecule so as to generate a directed, recombinant fusion nucleic acid molecule.

Abstract: RsbW-1 polypeptides and DNA (RNA) encoding such RsbW-1 and a procedure for producing such polypeptides by recombinant techniques is disclosed. Also disclosed are methods for utilizing such RsbW-1 for the treatment of infection, particularly bacterial infections. Antagonists against such RsbW-1 and their use as a therapeutic to treat infections, particularly bacterial infections are also disclosed. Also disclosed are diagnostic assays for detecting diseases related to the presence of RsbW-1 nucleic acid sequences and the polypeptides in a host. Also disclosed are diagnostic assays for detecting polynucleotides encoding SigB operon and for detecting the polypeptide in a host.

Abstract: A miniaturized multi-chamber thermocycler provides a thermocycler which is easy to handle, and permits the treatment of a great number of samples of small sample volumes at high temperature changing rates and at low heating powers. A sample receptacle body manufactured in micro-system technics provides a plurality of sample chambers which are embodied such that at least one of the sample chamber walls of the sample chamber which constitutes the sample chamber base is an efficient heat conductor and also of low mass. Said sample chambers are coupled to a coupling body, serving as heat sink, established via at least one poor heat conducting bridge which, with respect to its dimensioning and/or material selection is such that its specific heat conductance .lambda. is smaller 5 W/K.degree..multidot.m.

Abstract: Disclosed herein are genetic markers for favorable reproductive traits in animals such as litter size, and weaning weight. Methods for identifying such markers, and methods of screening animals to determine those more likely to produce favorable reproductive traits and preferably selecting those animals for future breeding purposes.

Abstract: Detector nucleic acids are employed for detection of nucleic acid target sequences by fluorescence quenching mechanisms. The detector nucleic acid comprises at least two oligonucleotides and is partially single-stranded and partially double-stranded. One of the two dyes of a donor/acceptor dye pair is linked to the first oligonucleotide and the other is linked to a second oligonucleotide such that they are in close spatial proximity when the first and second oligonucleotides are base-paired and donor fluorescence is quenched. A single second oligonucleotide may be hybridized to the first oligonucleotide or multiple second oligonucleotides may be hybridized to the first oligonucleotide and to each other, forming a junction structure comprising multiple donor/acceptor dye pairs. The detector oligonucleotide retains its partially single-stranded and partially double-stranded conformation in the absence of target.

Abstract: A gene is provided which is present in the deletion region of a chromosome common in lung cancer, hepatocellular carcinoma and colorectal cancer and encodes a novel protein, a protein encoded by the gene (PRLTS protein), and a method of discriminating tumor cells.

Abstract: A method for introducing a site-specific mutation into a target polynucleotide sequence is presented. The method involves the use of an oligonucleotide capable of binding to the target sequence, either by triplex formation (mediated by Hoogsteen, reverse Hoogsteen or equivalent base pairing) or by Watson/Crick base pairing (in the presence of a recombinase enzyme). The oligonucleotide of the invention is modified by the covalent attachment of one or more electrophilic groups. When a modified oligonucleotide is bound to its target sequence, the electrophilic group is able to interact with a nearby nucleotide in the target sequence, causing a modification to the nucleotide that results in a change in nucleotide sequence. Compositions used in the practice of the method are also disclosed.

Abstract: This invention is directed to a novel method for PCR amplification wherein PCR is carried out at a higher pH than the pH widely used in the art. Specifically, the buffer solution is adjusted to pH 9.0 to 11.0 at 25.degree. C. Using the present invention, DNA amplification can be successfully carried out following a simple pretreatment. In the present invention whole blood is mixed with a hypotonic solution so that a selective lysis of red blood cells takes place. The residual leukocytes are then collected. The leukocytes are mixed with a polymerization agent, primers and other necessary reagents and PCR is carried out. When the PCR solution is placed at a high temperature for DNA denaturation, the leukocytes are lysed so that the leukocyte DNA is released and can access the primers and the other necessary reactions for PCR in the solution.Cell membranes and proteins are present in the PCR reaction solution due to the lack of a protein extractive step during the pretreatment.

Abstract: The invention is directed to a method for sequencing multiple target polynucleotide segments in parallel, and to compositions and kits therefor. In the method, a plurality of sample polynucleotide fragments are used to form a mixture of different-length sequencing fragments. The sequencing fragments are complementary to at least two different sample fragments, wherein (1) each sequencing fragment terminates at a predefined end with a known base or bases, and (2) each sequencing fragment contains an identifier tag sequence that identifies the sample fragment to which the sequencing fragment corresponds. The sequencing fragments are then separated on the basis of size to produce a plurality of resolved, size-separated bands. Resolved bands are collected in separate aliquots, which, in a preferred embodiment, are then subjected to an amplification step to amplify the complements of the tag sequences in each aliquot, and preferably, the tag sequences too. Amplification is preferably by PCR.

Abstract: Filamentous microorganisms of improved properties, for example growth rate, may be obtained by culturing a sample of desired morphology until a substantial proportion of the culture diverges from that morphology, selecting an organism from the culture at that stage which exhibits the desired morphology and repeating the process with the selected microorganism. Furthermore, an isolated Fusarium graminearum having all of the characteristics of IMI 366464 and also possessing a greater morphological stability and growth rate than Fusarium graminearium strain IMI 145,425 is disclosed.

Abstract: The method of base sequence determination according to the present invention ensures an effective determination of a long DNA base sequence, by providing simultaneous determination of base sequences of two or more positions of the long DNA or base sequences of two or more DNAs, using the DNA probe chip which classifies and retains the DNA oligomers having various sequences, and using fluorophorelabeled primers which have the same sequencies as the oligomers in the chip and are labeled by various fluorophores, then followed by the extension of the determined base length by re-selection of the primers complementary to the sequence thus determined.

Abstract: An assay for detection of a mammalian cell proliferative disorder associated with a hypermutable nucleic acid sequences is provided. The identification of particular hypermutable sequences such as microsatellite loci correlates with a particular cancer, thereby allowing detection of both primary tumors and metastatic sites within a patient.

Abstract: The present invention describes methods of synthesizing oligonucleotides. In particular, it relates to methods of enzymatically synthesizing chirally pure oligonucleotides using templates which can be digested after synthesis. By using digestible templates, separation and purification of the synthesized oligonucleotides are greatly facilitated.

Abstract: A process for hydroxylating compounds of the formula ##STR1## where n, A and R.sup.1 to R.sup.4 have the meanings stated in the description, with the aid of microorganisms of the genus Beauveria.

Abstract: The present invention is directed to a process for amplifying and detecting any target nucleic acid sequence contained in a nucleic acid or mixture thereof and for assembling large polynucleotides from component polynucleotides, each involving generating concatemers formed by PCR amplification of overlapping fragments.

Abstract: The invention provides a human actVA-ORF4-like protein (A-ORFP) and polynucleotides which identify and encode A-ORFP. The invention also provides expression vectors, host cells, agonists, antibodies and antagonists. The invention also provides methods for treating disorders associated with expression of A-ORFP.

Abstract: The invention provides for a methods and compositions for identifying proteins or compounds that directly or indirectly modulate a genomic polynucleotide and methods for identifying active genomic polynucleotides. Generally, the method comprises inserting a BL (beta-lactamase) expression construct into an eukaryotic genome, usually non-yeast, contained in at least one living cell, contacting the cell with a predetermined concentration of a modulator, and detecting BL activity in the cell.

Abstract: Processes and kits for simultaneously amplifying and sequencing nucleic acid molecules, and perfonning high throughput DNA sequencing are described.

Abstract: A method of amplifying in vivo a DNA sequence B present in a genome of a parent cell, comprising (a) integrating in a genome of said cell a DNA construct comprising the structure C-M-A-D, in which both A and C denote a DNA sequence which is homologous with a genomic DNA fragment either flanking or overlapping the DNA sequence B, the sequence C being located in the opposite end the sequence B as compared to A, D denotes a DNA sequence which is homologous with a genomic DNA fragment located distal for C as compared to B, and M denotes a DNA sequence encoding a selection marker, (b) selecting for cells in which the DNA sequence M has been integrated in the genome, which cells comprise, in any orientation, the structure A-B-C-M-A-D and (c) propagating the cells selected in step (b) under increasing selection pressure to obtain a cell which has obtained an increased number of genomically integrated copies of the DNA sequences B and M.

Abstract: A method is provided for determining the identity of at least two discrete single bases each adjacent to a predetermined nucleotide base sequence in a target sample having one or more types of polynucleotide chain.

Abstract: A synthetic antifreeze peptide and a synthetic gene coding for the antifreeze peptide have been produced. The antifreeze peptide has a greater number of repeating amino acid sequences than is present in the native antifreeze peptides from winter flounder upon which the synthetic antifreeze peptide was modeled. Each repeating amino acid sequence has two polar amino acid residues which are spaced a controlled distance apart so that the antifreeze peptide may inhibit ice formation. The synthetic gene has been expressed in E. coli. A synthetic insert fragment has been prepared which can be readily inserted into the synthetic gene to alter the number of repeating units and/or amino acid composition in the antifreeze peptide produced.