Abstract: The present invention is directed to a process for the production of a peptide, polypeptide, or protein having a predetermined property. In accordance with one embodiment, the process begins by producing by way of synthetic polynucleotide coupling, stochastically generated polynucleotide sequences. A library of expression vectors containing such stochastically generated polynucleotide sequences is formed. Next, host cells containing the vectors are cultured so as to produce peptides, polypeptides, or proteins encoded by the stochastically generated polynucleotide sequences. Screening or selection is carried out on such host cells to identify a peptide, polypeptide, or protein produced by the host cells which has the predetermined property. The stochastically generated polynucleotide sequence which encodes the identified peptide, polypeptide, or protein is then isolated and used to produce the peptide, polypeptide, or protein having the predetermined property.

Abstract: A hybridization carrier, containing a single-stranded polynucleotide having the formula:5'-(dN).sub.n (dT).sub.m -3',wherein N represents admine, guanine or cytosin; T represents thymine; n is an integer of 2 or larger; and m is an integer of 5 or larger;the polynucleotide being immobilized by an amide bond on a surface of an organic polymers particle having a diameter of from about 0.05 .mu.m to about 5 .mu.m;the polynucleotide being immobilized at the site of a nucleotide sequence consisting of 2 or more polynucleotide which contain a primary amino residue in the polynucleotide; andthe amide bond having been formed between the primary amino residue and a carboxyl residue on the surface of the organic polymer particle.

Abstract: Disclosed are new nucleosome arrays that can be used in assays that couple the activity of a chromatin remodeling enzyme (or enzyme complex) to the activity of a restriction endonuclease to quantitatively measure the extent of "remodeling" activity exhibited by a particular remodeling enzyme or enzyme complex. Further, the new nucleosome arrays can be used in methods for screening candidate modulators, i.e., inhibitors or enhancers, of chromatin remodeling enzymes or enzyme complexes.

Abstract: A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Abstract: The invention relates to new methods of RNA isolation that exploit the surprising discovery that RNA may be differentially precipitated from DNA. The subject methods result in the formation of an RNA-containing precipitate that has an RNA content at least two fold enriched with respect to DNA, as compared with the RNA to DNA ratio of the solution from which the RNA-containing precipitate is derived. The invention also includes various methods of DNA isolation that employ the selective precipitation of RNA. The degree of RNA enrichment achieved is often much greater than two fold; enrichment by a factor of ten or greater is frequently obtained. By precipitating RNA from a solution, the RNA may be collected by simple procedures such as centrifugation or filtration, thereby avoiding the need to bind the RNA to solid phase. The collected RNA precipitate may then be solubilized.

Abstract: The invention features nucleic acid molecules and methods for use in site-specific methylation of ribonucleotides. The methods of the invention can be used to modulate RNA folding, RNA processing, RNA cleavage, and other processes involving sequence-specific recognition of RNA sequences, as well as for promoting RNA stability.

Abstract: The present invention provides a process for determining genotypes in highly polymorphic systems by polymerase chain reaction amplification of CDNA or genomic DNA and direct sequencing polymerase chain reaction products using oligonucleotide primers. More specifically, Class II and Class I HLA genotypes can be unambiguously determined in any subject in 16-24 hours by direct sequencing of DRB, DQB, DQA, DPB, DPA, HLA-A, HLA-B and HLA-C- transcripts enzymatically amplified using a limited number of non-allele-specific oligonucleotides. Total cellular RNA from peripheral blood mononuclear cells is reverse transcribed using antisense primers, specific for different locus (DQB, DQA, DPA or DPB) or group of loci (DRB1-5, or HLA-A and HLA-B and HLA-C). The synthesized cDNA molecules are then enzymatically amplified using different combinations of oligonucleotides for each locus and directly sequenced with Taq polymerase using an internal oligonucleotide. The sequenced genes are then analyzed.

Abstract: The present invention relates to the use of nucleic acid analogues in blocking nucleic acid amplification procedures and to diagnostic and analytical techniques based thereon. Also included are kits for use in the conduct of nucleic acid amplification reactions.

Abstract: A method of locating an inhibitory/instability sequence or sequences within the coding region of an mRNA and modifying the gene encoding that mRNA to remove these inhibitory/instability sequences by making clustered nucleotide substitutions without altering the coding capacity of the gene is disclosed. Constructs containing these mutated genes and host cells containing these constructs are also disclosed. The method and constructs are exemplified by the mutation of a Human Immunodeficiency Virus-1 Rev-dependent gag gene to a Rev-independent gag gene. Constructs useful in locating inhibitory/instability sequences within either the coding region or the 3' untranslated region of an mRNA are also disclosed. The exemplified constructs of the invention may also be useful in HIV-1 immunotherapy and immunoprophylaxis.

Abstract: The invention provides a human hydroxypyruvate reductase (HHPR) and polynucleotides which identify and encode HHPR. The invention also provides expression vectors, host cells, agonists, antibodies and antagonists. The invention also provides methods for treating disorders associated with expression of HHPR.

Abstract: The present invention relates to a composition which is useful for the reversible binding of a nucleic acid molecule. The composition, which may be packaged in a kit, includes a paramagnetic particle in an acidic solution.

Abstract: Phanerochaete chrysosporium strains CNCM numbers I-1511, I-1512 and I-1513 are found that produce increased amounts of manganese peroxidase (MnP) and lignin peroxidase (LiP). Immobilized cells may be used for culturing, and culture media is preferably supplemented with a phospholipid as a carbon source and/or veratryl alcohol to stabilize enzymes produced. Culturing conditions can be selected to modify the MnP/LiP ratio in favor of the production of MnP or LiP.

Abstract: The present invention provides novel methods for identifying gene expression patterns in mRNA populations. The methods are useful for determining differential gene expression among various cells or tissues, including cells or tissues of a target organism. The invention also provides methods of determining the frequency of gene expression in mRNA populations, thus providing a method of comparing gene expression frequency among various cells or tissues. The present invention also provides methods for isolating genes corresponding to tag sequences identified according to the methods of the present invention. Furthermore, sequences that are identified according to the present invention may be used to diagnose the presence of disease.

Abstract: A process for isolating polynucleotides from aqueous mixtures containing both polynucleotides and polysaccharides is described. The process uses polymer gels containing --B(OH).sub.2 groups, and is useful in purifying deoxyribonucleic acid extracted from plants.

Abstract: Nucleic acid sequences that are useful for detecting Legionella pneumophila are herein provided. These sequences can be used in hybridization assays or amplification based assays designed to detect the presence of Legionella pneumophila in a test sample. Additionally, the sequences can be provided as part of a kit.

Abstract: Compounds, compositions and methods are provided for inhibiting the expression of human HER-2 (also known as c-neu, ErbB-2 and HER-2/neu). The compositions comprise antisense oligonucleoptides targeted to nucleic acids encoding HER-2. Methods of using these oligonucleotides for inhibition of HER-2 expression and for treatment of diseases such as cancers associated with overexpression of HER-2 are provided. Methods of inhibiting other growth factor receptors using antisense oligonucleotides targeted to nucleic acids encoding HER-2 are also provided.

Abstract: The present invention relates to biological control of plant diseases and concerns new Gliocladium catenulatum fungi and their use for controlling fungal infections in plants. The invention concerns also compositions comprising new strains of Gliocladium catenulatum and their use to said purpose.

Abstract: The present invention is directed to extracorporeal cell systems infected with hepatitis C virus (HCV). The present invention also relates to products of such cell systems and their use as vaccines and in immunoassays. Methods whereby HCV-infected extracorporeal cell systems are constructed are included, and various immunoassays to detect HCV antibodies are also presented. The HCV-infected cell systems can be used to screen putative antiviral agents.

Abstract: A molecular detection device including a support member (36) and a plurality of molecular receptors (34) arranged at a plurality of sites of the support member (36). In a first aspect, the molecular receptors (34) are arranged in accordance with a mapping selected from the group consisting of a random mapping and a pseudorandom mapping. In a second aspect, data associated with the mapping is written to a member associated with the support member (36). In a third aspect, the molecular receptors (34) includes a first plurality of molecular receptors germane to an application and at least one molecular receptor extraneous to the application.

Abstract: A method is provided using centrifugation to prepare a seal of solidified wax, grease or polymer mix over an aqueous reagent in a reaction container such that the reagent is separated from contact with the atmosphere. The amount of solidified wax, grease or polymer mix is not sufficient when melted to a liquid to separate the reagent from contact with the atmosphere under gravity. A reagent and solidified wax, grease or polymer mix are combined in a container. During centrifugation and heating, the solidified wax, grease or polymer mix melts to a liquid, and centrifuging causes the liquid to form over the reagent a layer that completely separates the reagent from the atmosphere. As centrifugation continues, the liquid is cooled and solidified to form the seal. Additional reagents are preferably added on top of the seal such that when the container is heated and the seal melted the upper and lower reagents mix for reaction.

Abstract: The following description sets forth antisense (AS) oligonucleotides (ODNs) complementary to the primary transcript of the human c-fes protooncogene and their use to inactivate said transcript. All-trans retinoic acid (ATRA) is reported to be used as a differentiation inducer on cells pretreated with said AS-ODNs to induce apoptosis of leukemic blast cells.

Abstract: Compositions and methods are provided for modulating the expression of integrin .alpha.4. Antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding integrin .alpha.4 are preferred. Methods of using these compounds for modulating integrin .alpha.4 expression and for treatment of diseases associated with expression of integrin .alpha.4 are also provided.

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

Abstract: A system for isolating mRNAs as cDNAs employs a polymerase amplification method using at least two oligodeoxynucleotide primers. In one approach, the first primer contains sequence capable of hybridizing to a site immediately upstream of the first A ribonucleotide of the mRNA's polyA tail and the second primer contains arbitrary sequence. In another approach, the first primer contains sequence capable of hybridizing to a site including the mRNA's polyA signal sequence and the second primer contains arbitrary sequence. In another approach, the first primer contains arbitrary sequence and the second primer contains sequence capable of hybridizing to a site including the Kozak sequence. In another approach, the first primer contains a sequence that is substantially complementary to the sequence of a mRNA having a known sequence and the second primer contains arbitrary sequence.

Abstract: Novel polynucleotides and the proteins encoded thereby are disclosed.

Abstract: A novel method and device for transporting and/or monitoring a fluid in a multi-port device 400, 800, 1000 used in a microfluidic system is provided. The multi-port device includes a substrate having a novel channel configuration. A first channel region 413 having a first port and a second port for transporting fluid therebetween is defined in the substrate. A second channel region 421 having a first port and a second port for applying electric current for heating fluid or for monitoring a fluid parameter therebetween is also defined in the substrate. In some embodiments, the first channel intersects 407 with the second channel. The heating or monitoring aspect of the invention can be used with a variety of biological reactions such as PCR, LCR, and others.

Abstract: Methods of forming cationic liposome/nucleic acid complexes in which the complexes have a mean diameter of about 200 to about 300 nm are provided. The complexes are formed by combining a first solution of preformed cationic unilamellar liposomes with a mean diameter of from 100 to 150 nm, with a second solution of nucleic acid. Each of the solutions are equilibrated prior to mixing to temperatures of from 0.degree. C. to about 12.degree. C., preferably about 2.degree. C. to about 7.degree. C. The preformed cationic liposomes are typically prepared from an unsaturated cationic lipid, for example DODAC, DOTAP, DOTMA, DODAP, DMRIE, DORI, DOSPA and combinations thereof, and a neutral lipid, for example DOPE or cholesterol. The combination of the first and second solutions is typically carried out by gentle mixing over ice for a period of time of from about 10 to about 60 minutes.

Abstract: Disclosed is a process of performing Sexual PCR which includes generating random polynucleotides by interrupting or blocking a synthesis or amplification process to show or halt synthesis or amplification of at least one polynucleotide, optionally amplifying the polynucleotides, and reannealing the polynucleotides to produce random mutant polynucleotides. Also provided are vector and expression vehicles including such mutant polynucleotides, polypeptides expressed by the mutant polynucleotides and a method for producing random mutant polypeptides.

Abstract: Described are compositions and methods which allow for the efficient addition of a defined sequence at the 3'-end of a full-length cDNA in the course of first-strand cDNA synthesis from an mRNA template. A cDNA synthesis primer that is capable of annealing to mRNA is used to prime the first strand synthesis reaction. An oligonucleotide that is linked to the 5'-end of the mRNA serves as a short, extended template such that when the reverse transcriptase enzyme reaches the 5'-end of the mRNA, the enzyme switches templates and proceeds to transcribe through the end of the linked oligonucleotide. As a result, the single-stranded cDNA product which corresponds to the full-length mRNA, will have at the 3'-end a defined sequence which is complementary to the linked oligonucleotide. A conservative element in the oligonucleotide sequence responsible for this reaction can include 3 to 5 guanylic acid residues at the 3'-end of the oligonucleotide.

Abstract: The present invention pertains to methods for the synthesis and cloning of full-length cDNA, or cDNA fragments, that correspond to the complete sequence of 5'-ends of mRNA molecules. The method of the present invention comprises contacting RNA with a cDNA synthesis primer which can anneal to RNA, a suitable enzyme which possesses reverse transcriptase activity, and a template switching oligonucleotide under conditions sufficient to permit the template-dependent extension of the primer to generate an mRNA-cDNA hybrid. The template switching oligonucleotide hybridizes to the CAP site at the 5'-end of the RNA molecule and serves as a short, extended template for CAP-dependent extension of the 3'-end of the ss cDNA that is complementary to the template switching oligonucleotide.

Abstract: Disclosed are compositions comprising viral vectors derived from the paramyxovirus, simian virus 5 (SV5). The SV5 vectors of the present invention are designed so that the HN protein that binds to sialic acid is not expressed, and in certain embodiments a foreign membrane bound protein is expressed on the viral surface that targets the virus to particular cells or tissues. The vector then is able to deliver a toxin or cytotoxic agent to the target cell. Also disclosed are nucleic acid segments useful as viral genomes and methods of producing viral vectors.

Abstract: The present invention provides a human RNA bind-protein (HRNABP) and polynucleotides which identify and encode HRNABP. The invention also provides genetically engineered expression vectors and host cells comprising the nucleic acid sequences encoding HRNABP and a method for producing HRNABP. The invention also provides for antagonists or antibodies specifically binding HRNABP, and their use, in the prevention and treatment of diseases associated with expression of HRNABP. Additionally, the invention provides for the use of antisense molecules to polynucleotides encoding HRNABP for the treatment of diseases associated with the expression of HRNABP. The invention also provides diagnostic assays which utilize the polynucleotide, or fragments or the complement thereof, and antibodies specifically binding HRNABP.

Abstract: The use of oligodeoxynucleotides modified at the 3'-terminal internucleotide link as therapeutic agents by a method of hybridizing the modified oligonucleotide to a complementary sequence within a targeted mRNA and cleaving the mRNA within the RNA-DNA helix by the enzyme RNaseH to block the expression of the corresponding gene.

Abstract: Novel oligonucleotides for amplification and profiling of nucleic acid templates are disclosed. Enhancements of nucleic acid fingerprinting methods are disclosed.

Abstract: Methods of diagnosing glaucoma, and particularly primary congenital glaucoma, by detecting mutations in a gene associated with glaucoma, such as the CYP1B1 gene, are disclosed. Methods include hybridization analysis, such as Southern or Northern analysis, which use hybridization of a mutant nucleic acid probe to the gene associated with glaucoma; direct mutation analysis by restriction digest; sequencing of the gene associated with glaucoma; hybridization of an allele-specific oligonucleotide with amplified genomic DNA; or identification of the presence of mutant proteins encoded by the gene associated with glaucoma. Kits for use in diagnosis of glaucoma are also described. Methods of treatment of glaucoma, including administration of the protein encoded by the gene associated with glaucoma; administration of genes, gene constructs, or other nucleic acid constructs; or administration of other therapeutic agents, are additionally described.

Abstract: Methods for detecting the presence of Neisseria gonorrhoeae are described. These methods are based upon amplifying a portion of the Neisseria gonorrhoeae genome and detecting the presence of the amplified nucleic acid. Various sets of primers and detectors are disclosed. The disclosed primers and detectors can be used in Strand Displacement Amplification assays, thermal Strand Displacement Amplification Assays, and homogeneous, fluorescent real time thermal Strand Displacement Amplification assays to specifically detect the presence of Neisseria gonorrhoeae even in the presence of contaminating microorganisms and in the presence of human DNA.

Abstract: A method is provided for genotyping a target sequence at at least two allelic sites by a 5' nuclease amplification reaction. In one embodiment, the method includes performing a nucleic acid amplification on a target sequence having at least two different allelic sites using a nucleic acid polymerase having 5'.fwdarw.

Abstract: A method for treating diseases and symptoms caused by papillomaviruses is presented. The method comprises administering an effective amount of one or more 2',5'-oligoadenylates consisting of the structure: ##STR1## wherein R.sub.2 is PO.sub.4.sup.2- and R.sub.3 is OH, R.sub.2 and R.sub.3 are OH; and n=1 or n=2.

Abstract: New methods are provided for the amplification of a midivariant DNA containing an inserted target specific nucleic acid sequence(s) to enable detection of the presence of a target nucleic acid sequence in a test sample. One method employs midivariant DNA as a template for the synthesis of RNA catalyzed by QB replicase. Two midivariant DNA/probe conjugates including a nonreplicable portion of midivariant DNA and a target specific nucleic acid sequence (probe) are described. An amplification method including the steps of hybridization and ligation of the midivariant DNA/probe conjugates followed by replication of the DNA template has enabled detection of less than 200 template molecules. In a modified amplification method one of the midivariant DNA/probe conjugates further includes a RNA polymerase promoter sequence to enable transcription of the midivariant DNA template into RNA. The sequential ligation-transcription-replication method enables the detection of a single template molecule.

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

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

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of Cellular Inhibitor of Apoptosis-2. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Cellular Inhibitor of Apoptosis-2. Methods of using these compounds for modulation of Cellular Inhibitor of Apoptosis-2 expression and for treatment of diseases associated with expression of Cellular Inhibitor of Apoptosis-2 are provided.

Abstract: Two new isolates of the Hepatitis C virus (HCV), J1 and J7, are disclosed. These new isolates comprise nucleotide and amino acid sequences which are distinct from the prototype HCV isolate, HCV1. Thus, J1 and J7 provide new polynucleotides and polypeptides for use, inter alia, in diagnostics, recombinant protein production and vaccine development.

Abstract: The present invention is generally directed to microfluidic systems and methods of using such systems in the determination of the nucleotide sequence of target nucleic acid sequences (referred to herein as the "target"). In particular, the present invention provides methods and systems for determining the relative positions within a target nucleic acid sequence that are occupied by a given nucleotide, e.g., A, T, G or C, by separating mixtures of nested sets of fragments of the target nucleic acid, which sets each include fragments that terminate in a different given nucleotide.

Abstract: Compositions and methods are provided for the treatment and diagnosis of diseases associated with protein kinase C. Oligonucleotides are provided which are targeted to nucleic acids encoding PKC. Oligonucleotides specifically hybridizable with a translation initiation site, 5'-untranslated region or 3'-untranslated region are provided. Oligonucleotides specifically hybridizable with a particular PKC isozyme or set of isozymes are also provided. In preferred embodiments, the oligonucleotides contain one or more chemical modifications. Methods of modulating PKC expression and of treating animals suffering from disease amenable to therapeutic intervention by modulating protein kinase C expression using oligonucleotides targeted to PKC are disclosed.

Abstract: Novel polynucleotides and the proteins encoded thereby are disclosed.

Abstract: Disclosed are devices for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction. The devices comprise a substrate microfabricated to define a sample inlet port and a mesoscale flow system, which extends from the inlet port. The mesoscale flow system includes a polynucleotide polymerization reaction chamber in fluid communication with the inlet port which is provided with reagents required for polymerization and amplification of a preselected polynucleotide. In one embodiment the devices may be utilized to implement a polymerase chain reaction (PCR) in the reaction chamber (PCR chamber).

Abstract: Oligonucleotides and other macromolecules are provided which have increased nuclease resistance, substituent groups for increasing binding affinity to complementary strand, and subsequences of 2'-deoxy-erythro-pentofuranosyl nucleotides that activate RNase H. Such oligonucleotides and macromolecules are useful for diagnostics and other research purposes, for modulating the expression of a protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to oligonucleotide therapeutics.

Abstract: This invention relates to a fermentation process for high-yield production of plasmid DNA in E coli strains. In the disclosed process, a slow growth rate of cells is controlled and maintained by an automated nutrient feed scheme based on dissolved oxygen concentration (DOC) and pH. This controlled slow growth rate promotes high plasmid DNA stability during host cell replication. As a result, high yield production of plasmid DNA is achieved.

Abstract: The invention provides a process for the lysis of a culture of lactic acid bacteria, or a product containing such culture e.g. cheese, by means of a lysin through the in situ production of a homologous autolysin, or a heterologous autolysin obtainable from Gram-positive bacteria esp. from lactic acid bacteria. The gene encoding said autolysin is controlled by a promoter, preferably regulated by food-grade ingredients or parameters, to achieve an enhanced lysis after induction resulting in an enhanced production of total autolysin compared with the natural production lever of the homologous autolysin during fermentation or shortly thereafter. Other uses of the invention include preparing a mixture of peptides which are modified by peptidases freed after the lysis, using the autolysin as a bactericidal agent against spoiling bacteria or pathogenic bacteria for improving the shelf life of a product containing the lysed culture.