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Passive sampling methods for contaminated sediments: practical guidance for selection, calibration, and implementation.

ABSTRACT: This article provides practical guidance on the use of passive sampling methods (PSMs) that target the freely dissolved concentration (Cfree ) for improved exposure assessment of hydrophobic organic chemicals in sediments. Primary considerations for selecting a PSM for a specific application include clear delineation of measurement goals for Cfree , whether laboratory-based "ex situ" and/or field-based "in situ" application is desired, and ultimately which PSM is best-suited to fulfill the measurement objectives. Guidelines for proper calibration and validation of PSMs, including use of provisional values for polymer-water partition coefficients, determination of equilibrium status, and confirmation of nondepletive measurement conditions are defined. A hypothetical example is described to illustrate how the measurement of Cfree afforded by PSMs reduces uncertainty in assessing narcotic toxicity for sediments contaminated with polycyclic aromatic hydrocarbons. The article concludes with a discussion of future research that will improve the quality and robustness of Cfree measurements using PSMs, providing a sound scientific basis to support risk assessment and contaminated sediment management decisions.

SUBMITTER: Ghosh U

PROVIDER: S-EPMC4235463 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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Passive sampling methods for contaminated sediments: practical guidance for selection, calibration, and implementation.

Ghosh Upal U Kane Driscoll Susan S Burgess Robert M RM Jonker Michiel T O MT Reible Danny D Gobas Frank F Choi Yongju Y Apitz Sabine E SE Maruya Keith A KA Gala William R WR Mortimer Munro M Beegan Chris C

Integrated environmental assessment and management 20140206 2

This article provides practical guidance on the use of passive sampling methods (PSMs) that target the freely dissolved concentration (Cfree ) for improved exposure assessment of hydrophobic organic chemicals in sediments. Primary considerations for selecting a PSM for a specific application include clear delineation of measurement goals for Cfree , whether laboratory-based "ex situ" and/or field-based "in situ" application is desired, and ultimately which PSM is best-suited to fulfill the measu ...[more]

PMID: 24288273

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Project description:BackgroundWithin the last years, numerous reports described successful application of the CRISPR nucleases Cas9 and Cpf1 for genome editing in filamentous fungi. However, still a lot of efforts are invested to develop and improve protocols for the fungus and genes of interest with respect to applicability, scalability and targeting efficiencies. These efforts are often hampered by the fact that-although many different protocols are available-none have systematically analysed and compared different CRISPR nucleases and different application procedures thereof for the efficiency of single- and multiplex-targeting approaches in the same fungus.ResultsWe present here data for successful genome editing in the cell factory Thermothelomyces thermophilus, formerly known as Myceliophthora thermophila, using the three different nucleases SpCas9, FnCpf1, AsCpf1 guided to four different gene targets of our interest. These included a polyketide synthase (pks4.2), an alkaline protease (alp1), a SNARE protein (snc1) and a potential transcription factor (ptf1). For all four genes, guide RNAs were developed which enabled successful single-targeting and multiplex-targeting. CRISPR nucleases were either delivered to T. thermophilus on plasmids or preassembled with in vitro transcribed gRNA to form ribonucleoproteins (RNPs). We also evaluated the efficiency of single oligonucleotides for site-directed mutagenesis. Finally, we were able to scale down the transformation protocol to microtiter plate format which generated high numbers of positive transformants and will thus pave the way for future high-throughput investigations.ConclusionWe provide here the first comprehensive analysis and evaluation of different CRISPR approaches for a filamentous fungus. All approaches followed enabled successful genome editing in T. thermophilus; however, with different success rates. In addition, we show that the success rate depends on the respective nuclease and on the targeted gene locus. We finally present a practical guidance for experimental considerations aiming to guide the reader for successful implementation of CRISPR technology for other fungi.

Dataset Information

Passive sampling methods for contaminated sediments: practical guidance for selection, calibration, and implementation.

Publications

Passive sampling methods for contaminated sediments: practical guidance for selection, calibration, and implementation.

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