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We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

Saliva evidence can provide important information in the forensic investigation of sexual assaults. Presumptive tests for saliva, sometimes used to determine when to process for DNA evidence, rely on the enzyme α-amylase found in the liquid fraction of saliva, the degradation rates of which are not well known. It is possible, then, that DNA, found in the cellular fraction of saliva, may be present after the enzyme can no longer be detected. This project examined two different presumptive assays for saliva, the Radial Diffusion assay and the Rapid Stain Identification Series Test for Saliva (RSID) assay in order to compare the test positivity rates against the persistence of cellular DNA. Presumptive assays were tested at 7 different time points over the course of 68 hours (two subjects) and 93 hours (one subject) for saliva deposited on human skin, and at various time points for 40 days for saliva deposited on glass slides. On glass, both types of presumptive assays showed positive results, and sufficient DNA (∼0.045ng for Y-filer) was recovered up to day 40. On human skin, the test positivity of both presumptive assays and DNA recovery varied widely between subjects and with sample location on the subject. In the majority of cases (88%), DNA was recovered for at least 35 hours. In nearly half of cases (44%), sufficient DNA was recovered at either the same time point or after both presumptive assays no longer showed positive results. In all cases the RSID-Saliva assay outperformed the Radial Diffusion. The results of this study indicate that forensically-useful DNA does in fact remain on the skin after the presumptive assays are no longer positive. This may support the practice of routine DNA testing even when presumptive assays are negative or inconclusive.