Abstract: Complex multidimensional datasets generated by digital imaging spectroscopy can be organized and analyzed by applying software and computer-based methods comprising sorting algorithms. Combinations of these algorithms to images and graphical data, allow pixels or features to be rapidly and efficiently classified into meaningful groups according to defined criteria. Multiple rounds of pixel or feature selection may be performed based on independent sorting criteria. In one embodiment sorting by spectral criteria (e.g., intensity at a given wavelength) is combined with sorting by temporal criteria (e.g., absorbance at a given time) to identify microcolonies of recombinant organisms harboring mutated genes encoding enzymes having desirable kinetic attributes and substrate specificity. Restriction of the set of pixels analyzed in a subsequent sort based on criteria applied in an earlier sort (“sort and lock” analyses) minimize computational and storage resources.

Abstract: The present invention provides an instrument and methods for a multispectral optical technique that can simultaneously classify individual biological cells within mixed populations. This invention, known as Multispectral Taxonomic Identification (MTID), shows that microscopy can be combined with a software analysis program to measure and categorize the fluorescence and other spectroscopically identifiable signals from complex populations of cells in situ, without cultivation. The invention thus enables high-throughput screening of cells for taxonomic classification.

Abstract: Methods for identifying nucleic acid sequences that affect a cellular phenotype are disclosed. The method uses a reporter gene whose level of expression correlates with the phenotype in conjunction with a method or device for measuring the level of reporter expression. An expression library is introduced into the cells, and those cells exhibiting changes in reporter expression level are selected. Expression library inserts from the selected cells are isolated, thereby providing a sub-library enriched for sequences that affect the phenotype reflected by the reporter. Further rounds of sub-library introduction and cell selection may be carried out to provide additional enrichment. Sequences identified using this method may be used to ascertain the identity of additional molecules involved in generating the cellular phenotype.

Abstract: Methods and compositions for peptides or protein fragments displayed on scaffolds and libraries of sequences encoding peptides or protein fragments displayed on scaffolds that permit the properties of the library to be easily and quantitatively monitored are disclosed. The scaffold is a protein that is capable of emitting light. Thus, analysis of the expression of individual members of the library when they are expressed in cells may be carried but using instruments that can analyze the emitted light, such as a flow sorter (FACS), a spectrophotometer, a microtitre plate reader, a CCD, a fluorescence microscope, or other similar device. This permits screening of the expression library in host cells on a cell-by-cell basis, and enrichment of the library for sequences that have predetermined characteristics.

Abstract: The present invention relates to a chemically modified mutant protein including a cysteine residue substituted for a residue other than cysteine in a precursor protein, the substituted cysteine residue being subsequently modified by reacting the cysteine residue with a glycosylated thiosulfonate. Also, a method of producing the chemically modified mutant protein is provided. The present invention also relates to a glycosylated methanethiosulfonate. Another aspect of the present invention is a method of modifying the functional characteristics of a protein including providing a protein and reacting the protein with a glycosylated methanethiosulfonate reagent under conditions effective to produce a glycoprotein with altered functional characteristics as compared to the protein. In addition, the present invention relates to methods of determining the structure-function relationships of chemically modified mutant proteins.

Abstract: The present invention provides parallel methods for determining nucleotide sequences and physical maps of polynucleotides associated with sample tags. This information can be used to determine the chromosomal locations of sample-tagged polynucleotides. In one embodiment, the polynucleotides are derived from genomic DNA coupled to insertion elements. As a result, the invention also provides parallel methods for locating the integration sites of insertion elements in the genome.

Abstract: Improvements in calorimetric assays, surfaces for arraying microcolonies and instrument hardware for screening mutagenized enzymes and proteins in a solid phase format are presented. These improvements permit new enzyme activities to be screened. New filter membrane materials and formats for arraying the microcolonies provide higher throughput, better solvent resistance and ease of handling. Modifications to the instrument heating and illumination systems provide improved temperature control and a more compact, folded light path.

Abstract: To elucidate molecular mechanisms in learning and memory, the expression of mRNAs in brains of rabbitsundergoing eyeblink conditioning was analyzed. Infusion of the transcription inhibitor actinomycin D (ActD) into the cerebellar nuclei reversibly blocked learning but not performance of the CR. Differential display PCR (DD-PCR) analysis of cerebellar RNAs from trained and pseudo-trained rabbits identified a 207-bp band that was induced with learning. The fragment was used to isolate a cDNA from a &lgr;gt11 rabbit brain library containing a 1698-bp open-reading frame. The genomic sequence also has been obtained and is reported. The deduced amino acid sequence contains the KKIAMRE motif, which is conserved among cdc2-related kinases. These results suggest that there is a new category of cdc2-related kinases in the brain whose function may be important in learning and memory.