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sted for the presence of E. coli, which is ” known to grow naturally in the Hawaiian environment and is expected to be readily detectable in all samples. In each 25 mL reaction, 3 mL sample DNA were added to 22 mL PCR mixture containing 1X Taq reaction buffer, 2.5 mM MgCl2 solution, 200 nM dNTP mixture, 0.1 mg/mL BSA, 400 nM of each primer , and 2 units of Taq polymerase. The amplification cycle consisted of an initial 5 min. denaturation at 94uC, followed by 35 cycles of 30 sec. denaturation at 94uC, 30 sec. annealing at 60uC, and 30 sec. extension at 72uC, completed by a final 5 min. extension at 72uC. Gel electrophoresis was performed as described above. Condition 1. Tanneal 2. 3. 4. BSA a Test Range 5060uCa, 2u increments 1.5, 2.0, 3.0, 4.0 mM 200, 400, 600, 800, 1000 nM Presence/Absence 40-50uC was 1828859 included if reported Tanneal in literature was,50uC. doi:10.1371/journal.pone.0032442.t002 a clear, positive detection signal, visualized by performing gel electrophoresis after PCR amplification. Validation through Screening of Sewage and Environmental Waters The primer set exhibiting the highest sensitivity, EQ-1/EQ-2, was confirmed using cDNA obtained from the three sewage stages described earlier. This set was selected as the optimal candidate for surveillance of EnV presence in the environment; the twenty-two environmental water samples were then tested for EnV contamination using the newly-optimized PCR conditions. PCR Product order DCC-2618 sequencing and Analysis In order to confirm true EnV detection and identify enteroviral strains present in the Hawaiian environment, selected positive DNA fragments amplified by primer set EQ-1/EQ-2 from sewage, water, and shellfish samples were subjected to DNA sequencing. DNA bands were excised from the 2% agarose gel and recovered using the QIAquick Gel Extraction kit, according to the manufacturer’s instructions. Recovered DNA samples from sewage and water were eluted using 30 mL EB buffer and cloned into pCRH2.1-TOPOH vectors using the TOPO TA CloningH kit according to the manufacturer’s instructions. 8 positive clones from a single influent sewage sample and 5 environmental clones from 5 positive sampling sites were submitted with the M13 forward primer, provided by the commercial kit, to the College of Natural Sciences Advanced Studies of Genomics, Proteomics and Bioinformatics for DNA sequencing. Recovered enteric viral DNA amplified from shellfish collected at 3 sampling sites was submitted for direct sequencing to the same facility. Resulting genomic sequences were aligned and compared with all available EnV sequences listed in the National Center for Biotechnology Information databank using the Basic Local Alignment Search Tool. Shellfish as Potential Indicators of Water Quality From nine of the beaches where water samples were obtained, marine bivalves Isognomon spp. were collected from reef crevices and from underneath rocks. Between 18 and 55 specimens were collected from each site, depending on size and availability. No specific permits were required for specimen collection. Following transport to the laboratory on ice, shellfish were immediately shucked, and nucleic acids were extracted from internal digestive tissues in 1.02.0 g aliquots using the MoBio PowerSoil RNA Isolation KitDNA Elution Accessory Kit, according to the manufacturer’s instructions. Extracted RNA was DNase-trested using the RTS DNase Kit, according to the manufacturer’s instructions. Nucleic acids were stored at 80uC.a As det