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Selph, KE, Karl DM, Landry MR.  1993.  Quantification of chemiluminescent DNA probes using liquid scintillation counting. Analytical Biochemistry. 210:394-401.   10.1006/abio.1993.1213   AbstractWebsite

A novel method for quantifying chemiluminescent DNA probes is described. The method uses liquid scintillation counting to measure light emission from the alkaline phosphatase-catalyzed breakdown of the substrate PPD (3-(4-methoxyspiro[1,2-dioxetane-3,2′-tri-cyclo[,7]decan]-4-yl)phenyl phosphate) on dot blot preparations. Serial dilutions of either pUC18 DNA or λ DNA were hybridized with digoxigenin-labeled probes and detected using the method described. Light flux (luminescence) was linearly related to DNA concentration, typically with a coefficient of determination (r2) of 0.9 or better. Due to the stability of alkaline phosphatase and the long-lived luminescence of PPD in the Lumi-phos formulation, repetitive analyses of a given sample can be made for up to 20 h. The method can reliably detect 17 amol of DNA (30 pg pUC18 DNA) with a coefficient of variation on replicate samples of 14%. Optimization experiments showed that 7% sodium dodecyl sulfate in the prehybridization and hybridization buffers resulted in the lowest background; the best combination of signal-to-noise ratio and reproducibility was obtained using Bio-Rad Zeta-Probe GT nylon membranes. Direct immersion of samples into a solution of substrate was found to give the most precise results and ensured that substrate limitation at high concentrations of alkaline phosphatase (i.e., higher DNA amounts) did not occur.

Hannides, CCS, Popp BN, Landry MR, Graham BS.  2009.  Quantification of zooplankton trophic position in the North Pacific Subtropical Gyre using stable nitrogen isotopes. Limnology and Oceanography. 54:50-61.   10.4319/lo.2009.54.1.0050   AbstractWebsite

We quantify the trophic positions of subtropical open-ocean zooplankton species using amino acid-specific (AA) stable nitrogen isotopic compositions. We model animal trophic position by computing trophic (15)N enrichment of glutamic acid relative to phenylalanine, and find that trophic position for primary copepod consumers (Oithona spp., Neocalanus robustior) and secondary copepod consumers (Pleuromamma xiphias and Euchaeta rimana) varied little over a 5-10-yr period in the North Pacific Subtropical Gyre (NPSG; mean +/- SD: 2.1 +/- 0.1 and 2.9 +/- 0.1, respectively). Comparison of AA (15)N enrichment patterns in different copepod species suggests that trophic (15)N enrichment is most consistent in glutamic acid, aspartic acid, and alanine, "trophic" AAs that are intimately involved in the citric acid cycle and energy production. We further test equations involving these trophic AAs and "source" AAs ( which appear to retain the nitrogen isotopic composition of the food-web base), and find that such compound-specific models give results that are identical to those calculated using whole-animal (bulk) stable isotopic compositions. However the benefits of our AA-based approach (i.e., the relatively few samples needed for precise TP estimation, elimination of the need for concurrent prey isotopic analyses, and the ability to utilize formalin-preserved specimens from archived collections), make this a powerful technique for the quantitative assessment of trophic position within the pelagic food web. We further discuss how stable isotopic analyses provide a new perspective on the structure of open-ocean food webs and can be used to trace large seasonal fluctuations in nitrogen source in the NPSG.