Abstract: Biomarkers for sepsis and resulting mortality can be detected by assaying blood samples. Changes in the concentration of the biomarkers can be used to indicate sepsis, risk of sepsis, progression of sepsis, remission from sepsis, and risk of mortality. Changes can be evaluated relative to data sets, natural or synthetic or semisynthetic control samples, or patient samples collected at different time points. Some biomarkers' concentrations are elevated during disease and some are depressed. These are termed informative biomarkers. Some biomarkers are diagnostic in combination with others. Individual biomarkers may be weighted when used in combinations. Biomarkers can be assessed in individual, isolated or assays, in parallel assays, or in single-pot assays.

Abstract: The present invention relates generally to a method of amplifying closed circular nucleic acid probes and, more particularly, to a method of amplifying closed circular nucleic acid probes by rolling circle amplification. The method of the present invention is useful in a range of applications involving the detection of nucleic acid sequences such as, but not limited to, the identification of genetic disorders, genetic variants or the presence of microbiological or viral agents.

Abstract: We measured the levels of 78 different cytokines and growth factors in culture supernatants to determine the cytokine profiles of cells treated with PARC. We found that specific cytokines were suppressed by PARC. PARC can be used to treat diseases such as cancer, autoimmune diseases, rheumatoid arthritis, myeloproliferative disorders, and coronary artery disease, which are characterized by too much mitosis.

Abstract: Disclosed is a method and compositions for the sensitive detection of the amount and location of specific nucleic acid sequences. The method makes use of a branched oligomer, referred to as a lollipop oligomer, that has a tail portion, a right arm portion, and a left arm portion. These three components are joined at a common junction making a three-tailed structure. The two arms each end with sequences complementary to adjacent sequences in a target sequence. This allows the right and left arms to be ligated together when the oligomer is hybridized to the target sequence, thus topologically linking the oligomer to the target sequence. The tail portion can then be detected at the location of the target sequence.

Abstract: Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The disclosed method generally involves replication of a target sequence such that, during replication, the replicated strands are displaced from the target sequence by strand displacement replication of another replicated strand. In one form of the disclosed method, the target sample is not subjected to denaturing conditions. It was discovered that the target nucleic acids, genomic DNA, for example, need not be denatured for efficient multiple displacement amplification. The primers used can be hexamer primers. The primers can also each contain at least one modified nucleotide such that the primers are nuclease resistant. The primers can also each contain at least one modified nucleotide such that the melting temperature of the primer is altered relative to a primer of the same sequence without the modified nucleotide(s). The DNA polymerase can be &phgr;29 DNA polymerase.

Abstract: Genomic or cDNA, or fragments and mixtures thereof, can be screened by generation of subsets and then subjecting the subsets to mismatch scanning procedures. Alternatively, DNA fragments can be generated by cutting with a restriction endonuclease that generates variable overhangs. For either of the above methods, Y-shaped adapters having a region of non-complementary single-stranded DNA at the end can be used. Heterohybrid DNA, containing one DNA strand derived from each of two different samples, or homohybrids, containing DNA strands from the same sample, can be selected. Adapters attached to the ends of the fragments are designed to allow the selective isolation of homohybrid or heterohybrid DNA.

Abstract: DNA containing nucleotide base mispairs can be isolated using a modified rolling circle amplification procedure. Specific Y-shaped adapters permit the selective circularization of these fragments with a complementary splint oligonucleotide. Rolling circle amplification is then carried out with a DNA polymerase. Rolling circle amplification can also be carried out using a mixture of DNA circles having different lengths. Genetic phase of linked DNA markers can be determined by selective amplification of one parental haplotype. DNA fragments can also be converted into a form that can be utilized as rolling circle amplification templates by ligation of hairpin forming adapters to the ends of the fragments. Two or more DNA polymerases can be used in a rolling circle amplification reaction. DNA polymerase III has special properties that improve rolling circle amplification.

Abstract: A general method for screening genomic or cDNA, or fragments and mixtures thereof, involves sample simplification by the generation of subsets and then subjecting the subsets to a modified mismatch scanning procedure that eliminates DNA having single stranded breaks after a MutSLH cleavage. The methods are particularly useful in human population isolates, including identification of identical-by-descent sequences, genomic comparisons of two or more individuals, and genomic comparisons of two populations of individuals, for the identification of sequences of low polymorphism.