Abstract: A portable system for real time detection of the presence of an infectious agent in a biological sample employs a reagent which detects the presence of a specific infectious agent in the sample, and emits a detectable signal when the reagent reacts with the sample and detects the presence of the infectious agent. A test cartridge has a reaction chamber for receiving the sample and the reagent. The reaction chamber has a predetermined internal geometry and at least one inner surface. Introducing the sample and the reagent into the test cartridge mixes the sample and the reagent. A testing unit receives the test cartridge, and includes a sensor for detecting an emitted detectable signal. The detection of the emitted detectable signal is indicative of the presence of the infectious agent in the sample.

Abstract: Graphical displays are provided of translational kinetics values of codon pairs in a host organism plotted as a function of polypeptide-encoding nucleotide sequence. Such translational kinetics values of codon pair frequencies correspond to the predicted translational pausing properties of a codon pair in a host organism. The graphical displays provided reflect the relative over-representation or under-representation of each codon pair in an organism, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide by comparing graphical displays of different codon pairs in sequences encoding the polypeptide. The graphical displays of translational kinetics values also can display codon pair properties on comparable numerical scales, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide in different organisms by comparing comparably scaled graphical displays of the same or different codon pairs in sequences encoding the polypeptide.

Abstract: Provided are methods for calculating codon pair translational kinetics values, creating a synthetic gene for expression in a host organism, and providing codon pair translational kinetic values. The methods typically are directed to refinement of statistical observed versus expected codon pair frequencies using one of several factors such as amino acid sequence homology, secondary or tertiary structural considerations, and empirical measurements. In some synthetic genes codon pairs are predicted not to cause a translational pause in the host organism, thereby providing a polynucleotide sequence encoding the desired polypeptide with desired translational kinetics properties. The methods can be performed using multiple parameter nucleotide sequence optimization methods, such as branch-and-bound methods for nucleotide sequence refinement.

Abstract: The invention is a general method for improving the performance of the DNA-based vaccines. The method utilizes a complex DNA-generated profile of antigens to extend the effects of DNA-based vaccines and to broaden the immune response. This broadened immune response in turn improves the protection of the recipient from divergent (but related) strains of a pathogen. In addition, it effectively improves the efficacy of DNA-based vaccines used for treatment of viral diseases, including acquired immunity disorder (AIDS). One embodiment, where the target viral pathogen is HIV (the causative agent for aids), the method identifies an orderly set of plasmids of related sequences that may be used to prime a broad and strong immune response to HLA-restricted viral antigens. This mixture of plasmids is thus capable of priming an appropriate immune response to reduce the viral burden in HIV infected patients or to protect uninfected patients from HIV infection.

Abstract: A substantially water-soluble polymer comprises a homopolymer or a copolymer and a first subunit precursor. The first subunit precursor comprises a first nucleic acid and an ethylene-containing moiety. The first subunit precursor is either covalently or non-covalently linked to the homopolymer or copolymer. The ethylene group is preferably tethered to the 3?- or 5?-hydroxyl position of the first nucleic acid. The substantially water-soluble polymer may further comprise a tissue-specific targeting moiety and/or a bioactive compound encapsulated by the homopolymer or copolymer.