Chemical characteristics of dissolved organic matter in an oligotrophic subtropical wetland/estuarine ecosystem

Fluorescence properties of whole water samples and molecular characteristics of ultrafiltrated dissolved organic matter (UDOM > 1,000 D) such as lignin phenol and neutral sugar compositions and 13C nuclear magnetic resonance (NMR) spectra were determined along a freshwater to marine gradient in Everglades National Park. Furthermore, UDOM samples were categorized by hierarchical cluster analysis based on their pyrolysis gas chromatography/mass spectrometry products. Fluorescence properties suggest that autochthonous DOM leached/exuded from biomass is quantitatively important in this system. 13C NMR spectra showed that UDOM from the oligotrophic Taylor Slough (TS) and Florida Bay (FB) ecosystems has low aromatic C (13% ± 3% for TS; 2% ± 2% for FB) and very high O-alkyl C (54% ± 4% for TS; 75% ± 4% for FB) concentrations. High O-alkyl C concentrations in FB suggest seagrass/phytoplankton communities as dominant sources of UDOM. The amount of neutral sugars was not appreciably different between the TS and FB sites (115 ± 12 mg C g C-1 UDOM) but their concentrations suggest a low level of diagenesis and high production rates of this material in this oligotrophic environment. Total yield of lignin phenols (vanillyl + syringyl phenols) in TS was low (0.20–0.39 mg 100 mg C-1 UDOM) compared with other riverine environments and even lower in FB (0.04–0.07 mg 100 mg C-1 UDOM) and could be a result of photodegradation and/or dilution by other utochthonous DOM. The high O-alkyl and low aromatic nature of this UDOM suggests significant biogenic inputs (as compared with soils) and limited bioavailability in this ecosystem.

The Effect of Sample and Sample Matrix on DNA Processing: Mechanisms for the Detection and Management of Inhibition in Forensic Samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

The effect of sample and sample matrix on DNA processing: Mechanisms for the detection and management of inhibition in forensic samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.^