Abstract: Method for characterizing, classifying and differentiating tissues and cell types, for predicting the behavior of tissues and groups of cells, and for identifying genes with changed expression. The method involves obtaining genomic DNA from a tissue sample, the genomic DNA subsequently being subjected to shearing, cleaved by means of a restriction endonuclease or not treated by either one of these methods. The base cytosine, but not 5-methylcytosine, from the thus-obtained genomic DNA is then converted into uracil by treatment with a bisulfite solution. Fractions of the thus-treated genomic DNA are then amplified using either very short or degenerated oligonucleotides or oligonuclcotides which are complementary to adaptor oligonucleotides that have been ligated to the ends of the cleaved DNA.

Abstract: The present invention relates to molecular motors and their use in linear analysis of polymers. In particular, molecular motors are used to move polymers with respect to a station such that specific signals arise from the interaction between the polymer and an agent at the station.

Abstract: A semiconductor nanocrystal compound is described which is capable of linking to one or more affinity molecules. The compound comprises (1) one or more semiconductor nanocrystals capable of, in response to exposure to a first energy, providing a second energy, and (2) one or more linking agents, having a first portion linked to the one or more semiconductor nanocrystals and a second portion capable of linking to one or more affinity molecules. One or more of these semiconductor nanocrystal compounds are linked to one or more affinity molecules to form a semiconductor nanocrystal probe capable of bonding with one or more detectable substances in a material being analyzed, and capable of, in response to exposure to a first energy, providing a second energy.

Abstract: The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped into basis genesets according to the co-regulation of their expression. Expression of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes are then used as the basis for comparison and detection of biological responses with greatly enhanced sensitivity.

Abstract: A system and corresponding method analyzes data for patterns, such as data produced from DNA sequencers. An ASCII text file, generated by DNA sequencer software, is used as the input source for the pattern analysis software program. This text file contains peak intensity data, identified by gel-lane and mobility, for bands corresponding to 2 sequences of differing length. The software uses gel-mobility values of control DNA samples to identify bands of interest from test samples in the dataset. Spurious data point or artifacts are filtered out in this selection process. The selected data is then imported to a second software program that performs algorithms such as linear progression and curve fitting.

Abstract: The present invention is a computerized method of identifying self-hybridizing sequences in nucleic acid strands. Once the sequences are identified, genetic information frequently residing in or near the sequences can be more easily identified. A computer program is used to automatically and rapidly conduct the steps of the method. Under the method, a practical minimum possible length of a stem sequence is first determined and entered into a program. A maximum loop size is then determined and entered. Subsequently, a mismatch factor is determined as well as whether to include G-T base pairs in total energy calculations. The calculations are then made by identifying a potential upstream stem sequence and iterating through possible downstream stem sequences. Once all possible downstream stem sequences have been compared to the upstream sequence, the upstream sequence is incremented by one base location, and once again all possible downstream sequences are compared.

Abstract: A method for the amplification of a target nucleic acid is disclosed comprising the steps of reacting a nucleic acid with an amplification reaction mixture and a modified thermostable enzyme, wherein said modified thermostable polymerase is prepared by a reaction of a mixture of a thermostable polymerase and a chemical modifying reagent. The chemical modification reagent is an aldehyde, preferably formaldehyde. Essentially complete inactivation of the enzyme at ambient temperatures is achieved, with recovery of enzymatic activity at temperatures above 50° C.

Abstract: A method comprising administering a PEG12000-IFN alpha conjugate to an individual afflicted with a viral infection susceptible of treatment with interferon alpha, preferably chronic hepatitis C, is disclosed.

Abstract: Methods are provided for diagnosing cancers, drug-screening, and functionally analyzing mutations involving the WT1 gene. The methods involve use of the newly identified set of genes which are regulated by WT1 as well as by the set of genes which are regulated by WT1 fusions to EWS. Monitoring expression levels of these sets of genes can be used as an indicator of the genetic status of the gene. It can also identify which have similar effects on down-stream genes.

Abstract: The invention relates to a method of performing a chemical reaction between a reagent and a substrate, involving an acyl transfer mechanism, in the presence of an imidazole-based catalyst capable of forming a transition complex with the substrate. The catalytic imidazole function is provided by a chemical structure element comprising an optionally substituted imidazolyl group flanked on one or both sides by a group or groups capable of stabilizing the transition complex by molecular interaction with the acyl group. The invention also relates to such a designed chemical structure element, a method of producing it by recombinant DNA techniques and a vector therefor.

Abstract: Disclosed herein are methods for detecting complex protein interactions and protein functional relationships, and reagents for carrying out those methods.

Abstract: Disclosed here is a nucleic acid sequence encoding a recognition component of the N-end rule pathway. This nucleic acid sequence is characterized by the ability to specifically hybridize to the nucleic acid sequence of SEQ ID NO 1 under stringent hybridization conditions. Such conditions are defined below. Also disclosed is a nucleic acid sequence encoding a recognition component of the N-end rule pathway which is characterized by the ability to specifically hybridize to the nucleic acid sequence of SEQ ID NO 2 under stringent hybridization conditions. Also disclosed are DNA expression vectors containing nucleic acid sequences of the type described above, as well as cells transformed with such expression vectors. Further disclosed are applications for the compositions described above.

Abstract: New therapeutic uses for BPI protein products that involve treatment of subjects with a BPI deficiency condition, including selective BPI deficiency, and newborns, particularly BPI-deficient newborns.

Abstract: An apparatus for predicting a residual hormone concentration in a patient after a removal of a portion of the patient's glandular tissue which secretes the hormone, includes an input device constructed to receive a plurality of measured hormone concentrations corresponding to a plurality of human fluid samples taken from a patient at a plurality of sample times, respectively; and further includes a computer processor configured to iteratively calculate a residual hormone concentration. In accordance with one feature of the present invention, the computer processor is configured to generate data denoting a residual amount of glandular tissue that will remain in the patient after the removal of the portion of the patient's glandular tissue; and the apparatus further comprises an output device constructed to output the generated data denoting the residual amount of glandular tissue.

Abstract: A method for developing a valence correct molecular structure using cellular encoding in which a set of basic types are determined for a set of basic components of the valence correct molecular structure. Each of a set of development operators for developing the valence correct molecular structure are associated with one or more of the basic types and an organism having a tree arrangement of the development operators is generated by matching the basic types associated with connections among the development operators in the tree. The matching among typed development operators reduces the likelihood of creating an unfit organism. The development of a valence correct molecular structure using cellular encoding may be used in conjunction with genetic programming to evolve a molecular structure. The type matching reduces the likelihood of creating unfit child organisms, thereby increasing the likelihood and speed of convergence to a solution for a desired valence correct molecular structure.

Abstract: Disclosed are methods for the isolation and purification of high-titer recombinant adeno-associated virus (rAAV) compositions. Also disclosed are methods for reducing or eliminating the concentration of helper adenovirus in rAAV samples. Methods are disclosed that provide highly-purified rAAV stocks having titers up to about 10.sup.13 particles/ml at particle-to-infectivity ratios of less than 100 in processes that are accomplished about 24 hours or less.

Abstract: A method for determining the concentration of a light-emitting compound. An electric pulse is applied to a pair of current-delivering electrodes immersed in an electrolyte having positioned between the electrodes a conductor not in electronic contact with electrodes. As a result of the applied electric pulse, the light-emitting compound in electronic contact with the conductor luminesces in which the emitted light is measured and used to quantify the light-emitting compound.

Abstract: Methods and compositions related to AIDS are disclosed. Using the methods of the present invention, candidate compounds may be screened for the ability to inhibit reverse transcriptase of human immunodeficiency virus ("HIV RT"). Active HIV RT mutants may be detected by the disclosed methods. The present invention also discloses methods for screening for compounds that inhibit HIV RT obtained from an individual patient. In another aspect, methods for testing the biological effectiveness of candidate compounds for the inhibition of HIV RT in vivo are disclosed.

Abstract: The invention provide a mammalian nucleic acid molecule and fragments thereof. It also provides for the use of the mammalian nucleic acid molecule for the characterization, diagnosis, evaluation, treatment, or prevention of conditions, diseases and disorders associated with gene expression and for the production of a model system. The invention additionally provides expression vectors and host cells for the production of the protein encoded by the mammalian nucleic acid molecule.