Abstract: The present invention comprises a method to identify granulocytic cell genes that are differentially expressed upon exposure to a pathogen or in a sterile inflammatory disease by preparing a gene expression profile of a granulocytic cell population exposed to a pathogen or isolated from a subject having a sterile inflammatory disease and comparing that profile to a profile prepared from quiescent granulocytic cells. The present invention is particularly useful for identifying cytokine genes, genes encoding cell surface receptors and genes encoding intermediary signaling molecules. The invention also includes methods to identify a therapeutic agent that modulates the expression of at least one gene in a granulocytic population. Genes which are differentially expressed during neutrophil contact with a pathogen, such as a virulent bacteria, or that are differentially expressed in a subject having a sterile inflammatory disease are of particular importance.

Abstract: Methods and compositions are provided to obtain uniform amplification of nucleic acid templates having varied G+C contents by adding betaine and DMSO to the reaction mixture.

Abstract: Methods for simultaneously selecting binding site sequences for multiple DNA-binding proteins are provided. A source of DNA-binding proteins is mixed with oligonucleotide duplexes containing a randomized internal sequence. Bound oligonucleotides are isolated, amplified and analyzed, such as by DNA sequence analysis. The oligonucleotide duplexes are also used to identify and isolate DNA-binding proteins.

Abstract: The present invention is directed to an approach to study changes in gene expression by the selective PCR amplification and display of 3'-end restriction fragments of double stranded cDNAs.

Abstract: Methods are provided for isolating binding sites of DNA-binding proteins. An extract, such as a nuclear extract, containing DNA-binding proteins is mixed with oligonucleotide duplexes comprising a random sequence. Bound duplexes are isolated and amplified. Methods are also provided for identifying DNA-binding proteins using isolated binding sites.

Abstract: The present invention provides methods to analyze gene expression by selective PCR amplification and display of 3'-end restriction fragments of double stranded cDNAs.

Abstract: A probe capable of binding by homologous base pairing independently to a pair of gene regions bordering the upstream and downstream sides of a pair of infrequent restriction endonuclease sites separated by between about 20-2,000 kilibases on a section of linear DNA. The probe is produced, according to the method of the invention by digesting the DNA section to completion with the selected endonuclease, and ligating the resulting fragments under conditions which favor end-to-end circularization, and selecting digest fragments of the large circular molecules which have end to end junctions. Also disclosed are method for mapping and ordering the positions of such probes, using another set of linking probes which span such rate cutting sites.

Abstract: A 16.7 kilodalton membrane protein which is produced in mature, but no early-stage, T cells has been discovered. The protein has four distinct amphipathic domains, each having an amino acid composition which is predictive of an alpha helical structure that would be stable in a lipid bilayer. Each of these regions is flanked by a relatively polar domain whose amino acid sequence is predictive of .beta. pleat peptide regions. An antibody specific against one of the polar domains can be used to discriminate mature T-cells in a mixed-cell sample.

Abstract: A method is provided for isolating and identifying a recombinant clone having a DNA segment therein coding for at least one desired heterologous polypeptide, at least a short amino acid sequence of which is known, by effecting cDNA synthesis on a mixture of mRNAs containing the mRNA coding of the desired polypeptide, isolating the resultant cDNA mixture, inserting the resultant cDNA into recombinant cloning vehicles, transforming hosts with the vehicles, separating the transformants and isolating and identifying a recombinant clone containing a DNA segment which is homologous over at least a portion thereof to at least one oligonucleotide probe specific for the DNA segment; wherein the probe is an extension of the nucleotide sequence of an oligonucleotide primer having a nucleotide sequence complementary to a region of the target mRNA coding for a portion of the known amino acid sequence, and is complementary to a longer region of the target mRNA coding for a longer portion of the known amino acid sequence.

Abstract: A junction-fragment DNA probe, a DNA probe cluster, and methods of preparing and using the probe and cluster to study gene localization and organization. The probe includes first and second gene segments which are derived from first and second, single-copy genomic-DNA gene regions, respectively, separated from one another, in the genomic DNA strand, by a selected distance of between about 20 and 2,000 kilobases. The two segments in the probe are connected at a jThe invention was supported in part by the National Institute of Health grant #NIH CA-30938 and the Government has certain rights to the invention.

Abstract: A method is provided for isolating and identifying a recombinant clone having a DNA segment therein coding for at least one desired heterologous polypeptide, at least a short amino acid sequence of which is known, by effecting cDNA synthesis on a mixture of mRNAs containing the mRNA coding for the desired polypeptide, isolating the resultant cDNA mixture, inserting the resultant cDNA into recombinant cloning vehicles, transforming hosts with the vehicles, separating the transformants and isolating and identifying a recombinant clone containing a DNA segment which is homologous over at least a portion thereof to at least one oligonucleotide probe specific for the DNA segment; wherein the probe is an extension of the nucleotide sequence of an oligonucleotide primer having a nucleotide sequence complementary to a region of the target mRNA coding for a portion of the known amino acid sequence, and is complementary to a longer region of the target mRNA coding for a longer portion of the known amino acid sequence.