This work was funded by the European Union Seventh Framework Program FP7/2007-2013 under grant agreement no. 265721. The authors thank the RIKILT Institute for Food Safety (NL) for their support in this project.

Note: The following protocol describes the SPE performed on 100 ml water sample with C18 sorbent and elution with 50% v/v methanol. The enriched sample is diluted to reach 10% v/v methanol before analysis with an enzyme linked immunosorbent assay (ELISA) kit.
1. Preparing the Reagents
<ol>
	<li>Prepare the water samples
	<ol>
		<li>Prior to any other step, filter each 100 ml water sample with 0.2 &#181;m pore size filters.</li>
		<li>Spike the sample with desired concentration by diluting appropriate volume of reference solution into a volume of water. For example, prepare 100 ml of water sample with 100 ng/L of E2 by diluting 3.3 &#181;l of E2 reference solution at a concentration of 300 &#181;g/L. Dilute this solution ten times to get a sample spiked with 10 ng/L E2. Dilute this latter another ten times to obtain a sample of 100 ml with 1 ng/L E2.</li>
		<li>Place the filtered sample (unmodified or spiked) in a glass bottle with GL45 thread. Use the sample on the same day. Take a small fraction to be analyzed with the ELISA to estimate initial concentration.</li>
	</ol>
	</li>
	<li>Prepare 300 &#181;l of eluent by diluting methanol in de-ionized (di-) water to 50% v/v in a tight tube.</li>
</ol>
2. Preparation of the SPE Column
<ol>
	<li>Prepare a 20 mg/ml suspension of octadecyl-silica sorbent particles by adding first 1,600 &#181;l of methanol and then 400 &#181;l of di-water to 40 mg of reverse phase sorbent. Tightly close the lid and agitate with a vortex.</li>
	<li>Installing the bottom membrane in column
	<ol>
		<li>Select one Nylon membrane with pore size 11 &#181;m and place it on a double layer of anti-dust tissue. With a 3 mm diameter punch, cut two small parts in the membrane.</li>
		<li>Grab one of the small membranes with a flat-end filter forceps and place it on one side of the column.</li>
		<li>Screw the flat-bottom connector with the tube and tighten. The membrane is now in place and the sorbent can be added securely. Draw an arrow on the body of the column pointing towards the end where the membrane was placed.</li>
	</ol>
	</li>
	<li>Preparing the packed sorbent column
	<ol>
		<li>Secure the column on the holder with the arrow pointing towards the bottom. The column must be set as vertically as possible.</li>
		<li>Attach an empty 10 ml disposable syringe to the end of the tube of the column, by using the Luer-Lock connectors.</li>
		<li>Prepare a micro-pipette with a 20-200 &#181;l tip, set the volume to 100 &#181;l. This pipette tip format is adapted to the size of the sorbent column to be prepared. The procedure would be more difficult with larger pipette tips such as the ones used with 1 ml pipettes.</li>
		<li>Agitate the sorbent suspension with a vortex, and rapidly pipet 100 &#181;l in the center on the column. While injecting, aspirate gently all the pipetted solution trough the membrane by using the syringe with the other hand. At this stage, the solution filling the syringe must be clear of particles, and a particle bed can eventually be observed in the column.</li>
		<li>Repeat this process 2 more times by agitating the stock suspension between all pipetting steps to ensure homogeneous suspension of the particles in the solution. The resulting column contains 6 mg of sorbent.</li>
		<li>When the 300 &#181;l of suspension have been loaded and dried by aspirating with the syringe, keep the syringe in position and place the second Nylon membrane on the top by using the forceps with the other hand.</li>
		<li>Screw down the second connector with tube and dispose the syringe. The SPE column is ready for use.</li>
	</ol>
	</li>
</ol>
3. Preparing the System
<ol>
	<li>Tighten the SPE column on the device by using the Luer-Lock connectors. The arrow must be pointing to the same direction as the one shown on the device.</li>
	<li>Connect the bottle containing the sample to the device by screwing the provided GL45 safety cap on it.</li>
	<li>Load 200 &#181;l of eluent in the &#39;Eluent&#39; reservoir.</li>
	<li>Load 800 &#181;l of di-water in the &#39;Dilution&#39; reservoir.</li>
	<li>Place a bottle at the waste outlet to collect the processed water during extraction step. The format is not important but the volume needs to be sufficiently large with regard to the sample volume.</li>
	<li>Place a small vial at the sensor outlet with the minimum volume capacity of 1.5 ml. A maximum volume of 1 ml will be too small as bubbles will form at this outlet when collecting enriched eluent and dilution buffer.</li>
	<li>Verify the pressure regulator is in closed position by turning it manually, reverse-clockwise until further movement is not possible.</li>
</ol>
4. SPE with the Prototype
<ol>
	<li>Switch on the prototype by pressing the button on the back.</li>
	<li>Preparing the user interface and selecting the program
	<ol>
		<li>Open the user interface. Select the communication port of the computer to which the device is connected from the list, and click the button &#39;Next&#39;.</li>
		<li>Enter the values 580 for pset and 30 for dpset. The pump will adjust to maintain pressure in the pressurized system and reservoirs at 580 &#177; 30 mbar when running.</li>
		<li>Select the automated mode.</li>
		<li>In the automated mode corner, load the program file in the box &#39;configuration file path&#39;.</li>
	</ol>
	</li>
	<li>Adjusting the pressure regulator
	<ol>
		<li>Start the pump.</li>
		<li>Turn manually the pressure regulator until the value read for preg is inferior but close to 320 mbar.</li>
		<li>Stop the pump.</li>
	</ol>
	</li>
	<li>Starting the SPE procedure
	<ol>
		<li>Press &#39;start&#39; in the automated mode corner. The pump will switch on and the extraction, elution and dilution steps will automatically follow one another. The whole procedure for a 100 ml sample is performed in 50 min.</li>
		<li>Verify the value of preg. It must be in the range 320 - 350 mbar during the extraction step to ensure an optimal flow-rate.</li>
		<li>Close the small vial and store at 4-5 &#176;C in the dark until analysis. Perform analysis in the following 30 hr to prevent degradation of the analyte.</li>
		<li>Dispose of the processed water.</li>
	</ol>
	</li>
	<li>Cleaning the system 
	Note: After each extraction procedure the system needs to be cleaned to prevent cross-contamination.
	<ol>
		<li>Prepare a 10 ml solution of methanol 70% v/v in a GL 45 glass bottle.</li>
		<li>Unplug the SPE column and plug the tubing with connectors.</li>
		<li>In the automated mode, select the &#39;cleaning&#39; file and start it with same pressure settings.</li>
	</ol>
	</li>
</ol>
5. Detection of Estradiol Concentration with ELISA
<ol>
	<li>Prepare the calibration samples with concentrations as indicated in the protocol provided with the ELISA kit that is used. Prepare one calibration set with the same matrix as the sample, and one calibration set with methanol 10% v/v.</li>
	<li>Dispense the necessary amount of sample in the wells on the plate, according to manufacturer&#39;s instructions. Use calibration samples, unmodified and spiked water samples that were filtered but not processed with SPE, and enriched samples in methanol 10% v/v. Use 3 wells per sample to reduce the error associated with the assay.</li>
	<li>Follow the indications of the protocol that is provided with the kit for the addition of reactants, incubation time, washing and further reaction with the enzyme.</li>
	<li>Read the optical signal in each well according to the kit manufacturer&#39;s instructions with a plate reader instrument and collect the data.</li>
	<li>Use the software of the plate reader instrument to fit the calibration curves and determine the E2 concentration in the initial sample with same matrix, and in the enriched samples with methanol 10% v/v.</li>
</ol>

<ol><li>Chang, H. S., Choo, K. H., Choi, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+methods+of+identification%2C+analysis+and+removal+of+endocrine+disrupting+compounds+%28EDCs%29+in+water%5BTitle%5D)+AND+%22J.+Hazard.+Matter%22%5BJournal%5D)">The methods of identification, analysis and removal of endocrine disrupting compounds (EDCs) in water.</a> J. Hazard. Matter. 172, 1-12 (2009).</li>
<li>Azzouz, A., Souhail, B., Ballesteros, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Continuous+solid-phase+extraction+and+gas+chromatography-mass+spectrometry+determination+of+pharmaceuticals+and+hormones+in+water+samples%5BTitle%5D)+AND+%22J.+Chromatogr.+A%22%5BJournal%5D)">Continuous solid-phase extraction and gas chromatography-mass spectrometry determination of pharmaceuticals and hormones in water samples.</a> J. Chromatogr. A. 1217, 2956-2963 (2010).</li>
<li>Tomsikova, H., Aufartova, J., Solich, P., Novakova, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((High+sensitivity+analysis+of+female-steroid+hormones+in+environ-mental+samples%5BTitle%5D)+AND+%22Trends+Anal.+Chem%22%5BJournal%5D)">High sensitivity analysis of female-steroid hormones in environ-mental samples.</a> Trends Anal. Chem. 34, 35-58 (2012).</li>
<li>Ciofi, L., Fibbi, D., Chiuminatto, U., Coppini, E., Checchini, L., Del Bubba, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Fully+automated+on-line+solid+phase+extraction+coupled+to+high-performance+liquid+chromatography-tandem+mass+spectrometric+analysis+at+sub-ng%2FL+levels+of+selected+estrogens+in+surface+water+and+wastewater%5BTitle%5D)+AND+%22J.+Chromatogr.+A%22%5BJournal%5D)">Fully automated on-line solid phase extraction coupled to high-performance liquid chromatography-tandem mass spectrometric analysis at sub-ng/L levels of selected estrogens in surface water and wastewater.</a> J. Chromatogr. A. 1283, 53-61 (2013).</li>
<li>Robles-Molina, J., Lara-Ortega, F. J., Gilbert-Lopez, B., Garcia-Reyes, J. F., Molina-Diaz, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Multi-residue+method+for+the+determination+of+over+400+priority+and+emerging+pollutants+in+water+and+wastewater+by+solid-phase+extraction+and+liquid+chromatography-time-of-flight+mass+spectrometry%5BTitle%5D)+AND+%22J.+Chromatogr.+A%22%5BJournal%5D)">Multi-residue method for the determination of over 400 priority and emerging pollutants in water and wastewater by solid-phase extraction and liquid chromatography-time-of-flight mass spectrometry.</a> J. Chromatogr. A. 1350, 30-43 (2014).</li>
<li>Huang, C. H., Sedlak, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Analysis+of+estrogenic+hormones+in+municipal+waste+water+effluent+and+surface+water+using+enzyme-linked+immunosorbent+assay+and+gas+chromatography%2Ftandem+mass+spectrometry%5BTitle%5D)+AND+%22Environ.+Toxicol.+Chem%22%5BJournal%5D)">Analysis of estrogenic hormones in municipal waste water effluent and surface water using enzyme-linked immunosorbent assay and gas chromatography/tandem mass spectrometry.</a> Environ. Toxicol. Chem. 20, 133-139 (2001).</li>
<li>Hintemann, T., Schneider, C., Schöler, H. F., Schneider, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Field+study+using+two+immunoassays+for+the+determination+of+estradiol+and+ethinylestradiol+in+the+aquatic+environment%5BTitle%5D)+AND+%22Water+Res%22%5BJournal%5D)">Field study using two immunoassays for the determination of estradiol and ethinylestradiol in the aquatic environment.</a> Water Res. 40, 2287-2294 (2006).</li>
<li>Farré, M., Kuster, M., Brix, R., Rubio, F., Lopez de Alda, M. J., Barcelo, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comparative+study+of+an+estradiol+enzyme-linked+immunosorbent+assay+kit%2C+liquid+chromatography-tandem+mass+spectrometry%2C+and+ultra-performance+liquid+chromatography-quadrupole+time+of+flight+mass+spectrometry+for+part-per-trillion+analysis+of+estrogens+in+water+samples%5BTitle%5D)+AND+%22J.+Chromatogr.+A%22%5BJournal%5D)">Comparative study of an estradiol enzyme-linked immunosorbent assay kit, liquid chromatography-tandem mass spectrometry, and ultra-performance liquid chromatography-quadrupole time of flight mass spectrometry for part-per-trillion analysis of estrogens in water samples.</a> J. Chromatogr. A. 1160, 166-175 (2007).</li>
<li>Pu, C., Wu, Y. F., Yang, H., Deng, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Trace+analysis+of+contraceptive+drug+levonorgestrel+in+waste+water+samples+by+a+newly+developed+indirect+competitive+enzyme-linked+immunosorbent+assay+%28ELISA%29+coupled+with+solid+phase+extraction%5BTitle%5D)+AND+%22Anal.+Chim.+Acta%22%5BJournal%5D)">Trace analysis of contraceptive drug levonorgestrel in waste water samples by a newly developed indirect competitive enzyme-linked immunosorbent assay (ELISA) coupled with solid phase extraction.</a> Anal. Chim. Acta. 628, 73-79 (2008).</li>
<li>Van Emon, J. M., Gerlach, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+status+report+on+field-portable+immunoassay%5BTitle%5D)+AND+%22Environ.+Sci.+Technol%22%5BJournal%5D)">A status report on field-portable immunoassay.</a> Environ. Sci. Technol. 29 (7), 312A-317A (1995).</li>
<li>Farré, M., Brix, R., Barcelò, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Screening+water+for+pollutants+using+biological+techniques+under+European+Union+funding+during+the+last+10+years%5BTitle%5D)+AND+%22Trends+Anal.+Chem%22%5BJournal%5D)">Screening water for pollutants using biological techniques under European Union funding during the last 10 years.</a> Trends Anal. Chem. 24 (6), 532-545 (2005).</li>
<li>Schneider, C., Schöler, H. F., Schneider, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+novel+enzyme-linked+immunosorbent+assay+for+ethinylestradiol+using+a+long-chain+biotinylated+EE2+derivative%5BTitle%5D)+AND+%22Steroids%22%5BJournal%5D)">A novel enzyme-linked immunosorbent assay for ethinylestradiol using a long-chain biotinylated EE2 derivative.</a> Steroids. 69, 245-253 (2004).</li>
<li>Heub, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Automated+and+portable+solid+phase+extraction+platform+for+immuno-detection+of+17%CE%B2-estradiol+in+water%5BTitle%5D)+AND+%22J.+Chrom.+A%22%5BJournal%5D)">Automated and portable solid phase extraction platform for immuno-detection of 17β-estradiol in water.</a> J. Chrom. A. 1381, 22-28 (2015).</li>
<li>Petrovic, M., Eljarrat, E., Lopez de Alda, M. J., Barcelo, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Endocrine+disrupting+compounds+and+other+merging+contaminants+in+the+environment%3A+a+new+survey+on+new+monitoring+strategies+and+occurrence+data%5BTitle%5D)+AND+%22Anal.+Bioanal.+Chem%22%5BJournal%5D)">Endocrine disrupting compounds and other merging contaminants in the environment: a new survey on new monitoring strategies and occurrence data.</a> Anal. Bioanal. Chem. 378, 549-562 (2004).</li>
<li>Richardson, S. D., Ternes, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Water+analysis%3A+Emerging+contaminants+and+current+issues%5BTitle%5D)+AND+%22Anal.+Chem%22%5BJournal%5D)">Water analysis: Emerging contaminants and current issues.</a> Anal. Chem. 86, 2813-2848 (2014).</li>
</ol>

The authors have nothing to disclose.

A new method for the preparation of water samples followed by analysis using immunoassay was proposed. The instrument enables to perform solid phase extraction in an automated and user-friendly way.
The filtration of the water sample prior to its injection into the system is critical. Any particulates still present in the solution would potentially cause clogging of the fluidic network and obstruct the SPE column. Another important step is the preparation of the SPE column. The amount of parti...

Sample preparation is an important step in any analytical process. In particular, removal of matrix effects, diminution of interferences, and enrichment of the analyte are necessary to obtain precise results and reach low limits of detection. Endocrine disrupting compounds (EDCs) are of particular concern due to their action on the living organisms even when present at very low levels in the environment. The natural hormone 17&#946;-estradiol is present on the EU water pollution Watch List and prone to be added to the list of priority substances regulated under the European Water Framework Directive. Solid phase extraction (SPE) is commonly applied for the analysis of small pollutants in water, with both chemical 1-5 (chromatography, mass spectrometry) and immunological 6-9 detection methods. The latter gained interest in the field of environmental monitoring, as immunoassays are available in large variety of formats, are specific to the target analyte, and reach low limits of detection.6, 7, 10, 11 Various enzyme linked immunosorbent assays (ELISA) are commercially available and enable to analyze multiple samples at once on a multi-well plate. The procedure consists in successive reaction steps that can take a few hours. The final product of reaction can be detected optically to determine the concentration of the target molecule based on a calibration curve.
Classical SPE procedures include sorbent pre-conditioning, sample extraction, washing, elution, and concentration by evaporation of the eluent. The solvent used for dilution of this extract is chosen depending on the detection method. For immunological methods, the amount of organic solvent influences strongly the sensitivity of the method.12
In addition to the recovery and the pre-concentration performances, the method also needs to be simple and cost efficient. Automation of the procedure helps to reduce human-related errors. In our previous work 13 we introduced our prototype for automated SPE, and our method was applied to the analysis of the natural hormone 17&#946;-estradiol in sea water samples. With the present video we would like to highlight the technical advantages of our method compared to traditional off-line and on-line SPE, and its particular compatibility with detection by immuno-reactions. We describe the protocol applied to water samples for the detection of 17&#946;-estradiol. SPE is performed with octadecyl-silica (C18) sorbent phase and elution is performed with diluted methanol.

<table><tbody><tr><td>Filter membrane 0.2 &amp;mu;m pore size</td><td>Merck Millipore</td><td>GNWP04700</td><td>For sample filtration</td></tr><tr><td>Nylon membrane 11 &amp;mu;m pore size</td><td>Merck Millipore</td><td>NY1104700</td><td>For SPE column</td></tr><tr><td>Disposable biopsy punch 5 mm</td><td>Medical Budget</td><td>39302439</td><td></td></tr><tr><td>Nucleodur C18 ec&amp;nbsp;</td><td>Macherey Nagel</td><td>713550.01</td><td>50 &amp;mu;m particle diameter</td></tr><tr><td>Synthetic sea water</td><td>Sigma Aldrich</td><td>SSWS500-500ML</td><td></td></tr><tr><td>Methanol</td><td>VWR</td><td></td><td></td></tr><tr><td>17beta-estradiol standard</td><td>Enzo Life Science</td><td></td><td>300 ng/ml</td></tr><tr><td>17beta-estradiol ELISA kit</td><td>Enzo Life Science</td><td>ADI-900-008</td><td>96 wells, range 30 - 3,000 ng/L</td></tr></tbody></table>

a simple method for automated solid phase extraction of water samples for immunological analysis of small pollutants

A new method for solid phase extraction (SPE) of environmental water samples is proposed. The developed prototype is cost-efficient and user friendly, and enables to perform rapid, automated and simple SPE. The pre-concentrated solution is compatible with analysis by immunoassay, with a low organic solvent content. A method is described for the extraction and pre-concentration of natural hormone 17&#946;-estradiol in 100 ml water samples. Reverse phase SPE is performed with octadecyl-silica sorbent and elution is done with 200 &#181;l of methanol 50% v/v. Eluent is diluted by adding di-water to lower the amount of methanol. After preparing manually the SPE column, the overall procedure is performed automatically within 1 hr. At the end of the process, estradiol concentration is measured by using a commercial enzyme-linked immune-sorbent assay (ELISA). 100-fold pre-concentration is achieved and the methanol content in only 10% v/v. Full recoveries of the molecule are achieved with 1 ng/L spiked de-ionized and synthetic sea water samples.

Reproducibility of sorbent packing was evaluated by drying and weighting the pipetted sorbent in glass vials and the result is shown in Figure 1. Reproducibility of the time of injection was tested for 100 ml samples, as shown in Figure 2. Concentration in initial and pre-concentrated spiked samples were determined by using a commercial ELISA kit for 17&#946;-estradiol and are shown in Figure 3.
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Watch this Scientific Journal Video about A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants at JoVE.com

A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants

A protocol for the extraction and pre-concentration of estradiol from water samples by using an automated and miniaturized system is presented.

A new method for solid phase extraction (SPE) of environmental water samples is proposed. The developed prototype is cost-efficient and user friendly, and ...

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JoVE Journal

Environment

13.7K Views.  Centre Suisse d'Electronique et de Microtechnique. A protocol for the extraction and pre-concentration of estradiol from water samples by using an automated and miniaturized system is presented.

Video: A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants

Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples

Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. 
In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads.

This manuscript describes an automated gel size selection approach for purifying DNA fragments for next-generation sequencing. The Ranger Technology provides complete automation of the entire process of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments allowing for high-throughput and high quality next-generation sequencing libraries.

Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA ...

Characterization and Application of Passive Samplers for Monitoring of Pesticides in Water

Five different water passive samplers were calibrated under laboratory conditions for measurement of 124 legacy and current used pesticides. This study provides a protocol for the passive sampler preparation, calibration, extraction method and instrumental analysis. Sampling rates (RS) and passive sampler-water partition coefficients (KPW) were calculated for silicone rubber, polar organic chemical integrative sampler POCIS-A, POCIS-B, SDB-RPS and C18 disk. The uptake of the selected compounds depended on their physicochemical properties, i.e., silicone rubber showed a better uptake for more hydrophobic compounds (log octanol-water partition coefficient (KOW) &#62; 5.3), whereas POCIS-A, POCIS-B and SDB-RPS disk were more suitable for hydrophilic compounds (log KOW &#60; 0.70).

A protocol about the characterization and application of five different passive sampling devices is presented.

Five different water passive samplers were calibrated under laboratory conditions for measurement of 124 legacy and current used pesticides. This study ...

VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders

Benthic suspension feeders play essential roles in the functioning of marine ecosystems. By filtering large volumes of water, removing plankton and detritus, and excreting particulate and dissolved compounds, they serve as important agents for benthic-pelagic coupling. Accurately measuring the compounds removed and excreted by suspension feeders (such as sponges, ascidians, polychaetes, bivalves) is crucial for the study of their physiology, metabolism, and feeding ecology, and is fundamental to determine the ecological relevance of the nutrient fluxes mediated by these organisms. However, the assessment of the rate by which suspension feeders process particulate and dissolved compounds in nature is restricted by the limitations of the currently available methodologies. Our goal was to develop a simple, reliable, and non-intrusive method that would allow clean and controlled water sampling from a specific point, such as the excurrent aperture of benthic suspension feeders, in situ. Our method allows simultaneous sampling of inhaled and exhaled water of the studied organism by using minute tubes installed on a custom-built manipulator device and carefully positioned inside the exhalant orifice of the sampled organism. Piercing a septum on the collecting vessel with a syringe needle attached to the distal end of each tube allows the external pressure to slowly force the sampled water into the vessel through the sampling tube. The slow and controlled sampling rate allows integrating the inherent patchiness in the water while ensuring contamination free sampling. We provide recommendations for the most suitable filtering devices, collection vessel, and storing procedures for the analyses of different particulate and dissolved compounds. The VacuSIP system offers a reliable method for the quantification of undisturbed suspension feeder metabolism in natural conditions that is cheap and easy to learn and apply to assess the physiology and functional role of filter feeders in different ecosystems.

VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders

We introduce the VacuSIP, a simple, non-intrusive, and reliable method for clean and accurate point sampling of water. The system was developed and evaluated for the simultaneous collection of the water inhaled and exhaled by benthic suspension feeders in situ, to cleanly measure removal and excretion of particulate and dissolved compounds.

Benthic suspension feeders play essential roles in the functioning of marine ecosystems. By filtering large volumes of water, removing plankton and ...

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet. This method, therefore, provides three different fractions of specific molecular composition, which are fully compatible with common high throughput 'omics' technologies such as liquid chromatography (LC) or gas chromatography (GC) coupled to mass spectrometers. Even though the method was initially developed for the analysis of different plant tissue samples, it has proved to be fully compatible for the extraction and analysis of biological samples from systems as diverse as algae, insects, and mammalian tissues and cell cultures.

A protocol for comprehensive extraction of lipids, metabolites and proteins from biological tissues using one sample is presented.

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually ...

Biochemistry

Extraction and Characterization of Surfactants from Atmospheric Aerosols

Surface-active compounds, or surfactants, present in atmospheric aerosols are expected to play important roles in the formation of liquid water clouds in the Earth&#39;s atmosphere, a central process in meteorology, hydrology, and for the climate system. But because specific extraction and characterization of these compounds have been lacking for decades, very little is known on their identity, properties, mode of action and origins, thus preventing the full understanding of cloud formation and its potential links with the Earth&#39;s ecosystems.
In this paper we present recently developed methods for 1) the targeted extraction of all the surfactants from atmospheric aerosol samples and for the determination of 2) their absolute concentrations in the aerosol phase and 3) their static surface tension curves in water, including their Critical Micelle Concentration (CMC). These methods have been validated with 9 references surfactants, including anionic, cationic and non-ionic ones. Examples of results are presented for surfactants found in fine aerosol particles (diameter &#60;1 &#956;m) collected at a coastal site in Croatia and suggestions for future improvements and other characterizations than those presented are discussed.

Methods are presented for the targeted extraction of surfactants present in atmospheric aerosols and the determination of their absolute concentrations and surface tension curves in water, including their Critical Micelle Concentration (CMC).

Surface-active compounds, or surfactants, present in atmospheric aerosols are expected to play important roles in the formation of liquid water clouds in ...

A Modified EPA Method 1623 that Uses Tangential Flow Hollow-fiber Ultrafiltration and Heat Dissociation Steps to Detect Waterborne Cryptosporidium and Giardia spp.

Cryptosporidium and Giardia species are two of the most prevalent protozoa that cause waterborne diarrheal disease outbreaks worldwide. To better characterize the prevalence of these pathogens, EPA Method 1623 was developed and used to monitor levels of these organisms in US drinking water supplies 12. The method has three main parts; the first is the sample concentration in which at least 10 L of raw surface water is filtered. The organisms and trapped debris are then eluted from the filter and centrifuged to further concentrate the sample. The second part of the method uses an immunomagnetic separation procedure where the concentrated water sample is applied to immunomagnetic beads that specifically bind to the Cryptosporidium oocysts and Giardia cysts allowing for specific removal of the parasites from the concentrated debris. These (oo)cysts are then detached from the magnetic beads by an acid dissociation procedure. The final part of the method is the immunofluorescence staining and enumeration where (oo)cysts are applied to a slide, stained, and enumerated by microscopy.
Method 1623 has four listed sample concentration systems to capture Cryptosporidium oocysts and Giardia cysts in water: Envirochek filters (Pall Corporation, Ann Arbor, MI), Envirochek HV filters (Pall Corporation), Filta-Max filters (IDEXX, Westbrook, MA), or Continuous Flow Centrifugation (Haemonetics, Braintree, MA). However, Cryptosporidium and Giardia (oo)cyst recoveries have varied greatly depending on the source water matrix and filters used1,14. A new tangential flow hollow-fiber ultrafiltration (HFUF) system has recently been shown to be more efficient and more robust at recovering Cryptosporidium oocysts and Giardia cysts from various water matrices; moreover, it is less expensive than other capsule filter options and can concentrate multiple pathogens simultaneously1-3,5-8,10,11. In addition, previous studies by Hill and colleagues demonstrated that the HFUF significantly improved Cryptosporidium oocysts recoveries when directly compared with the Envirochek HV filters4. Additional modifications to the current methods have also been reported to improve method performance. Replacing the acid dissociation procedure with heat dissociation was shown to be more effective at separating Cryptosporidium from the magnetic beads in some matrices9,13 .
This protocol describes a modified Method 1623 that uses the new HFUF filtration system with the heat dissociation step. The use of HFUF with this modified Method is a less expensive alternative to current EPA Method 1623 filtration options and provides more flexibility by allowing the concentration of multiple organisms.

A Modified EPA Method 1623 that Uses Tangential Flow Hollow-fiber Ultrafiltration and Heat Dissociation Steps to Detect Waterborne Cryptosporidium and Giardia spp.

This protocol describes the use of a tangential flow hollow-fiber ultrafiltration sample concentration system and a heat dissociation as alternative steps for the detection of waterborne Cryptosporidium and Giardia species using EPA Method 1623.

Cryptosporidium and Giardia species are two of the most prevalent protozoa that cause waterborne diarrheal disease outbreaks worldwide. To better ...

Immunology and Infection

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Historical and emerging per- and polyfluoroalkyl substances (PFASs) have garnered significant interest from the public and government agencies from the local to federal levels. The continuing evolution of PFAS chemistries presents a challenge to the environmental monitoring, where ongoing development of targeted methods necessarily lags the discovery of new chemical compounds. There is a need, therefore, to have forward-looking methodologies that can detect emerging and unexpected compounds, monitor these species over time, and resolve details of their chemical structure to enable future work in human health. To this end, non-targeted analysis by high-resolution mass spectrometry offers a broad base detection approach that can be combined with almost any sample preparation scheme and provides significant capabilities for compound identification after detection. Herein, we describe a solid-phase extraction (SPE) based sample concentration method tuned for shorter chain and more hydrophilic PFAS chemistries, such as per fluorinated ether acids and sulfonates, and describe analysis of samples prepared in this fashion in both targeted and non-targeted modes. Targeted methods provide superior quantification when reference standards are available but are intrinsically limited to expected compounds when performing analysis. In contrast, a non-targeted approach can identify the presence of unexpected compounds and provide some information about their chemical structure. Information about chemical features can be used to correlate compounds across sample locations and track abundance and occurrence over time.

Here, we present a protocol for the sequential targeted quantification and non-targeted analysis of fluorinated compounds in water by mass spectrometry. This methodology provides quantitative levels of known fluorochemical compounds and identifies unknown chemicals in related samples with semi-quantitative estimates of their abundance.

Historical and emerging per- and polyfluoroalkyl substances (PFASs) have garnered significant interest from the public and government agencies from the ...

Fabrication of a Dipole-assisted Solid Phase Extraction Microchip for Trace Metal Analysis in Water Samples

This paper describes a fabrication protocol for a dipole-assisted solid phase extraction (SPE) microchip available for trace metal analysis in water samples. A brief overview of the evolution of chip-based SPE techniques is provided. This is followed by an introduction to specific polymeric materials and their role in SPE. To develop an innovative dipole-assisted SPE technique, a chlorine (Cl)-containing SPE functionality was implanted into a poly(methyl methacrylate) (PMMA) microchip. Herein, diverse analytical techniques including contact angle analysis, Raman spectroscopic analysis, and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) analysis were employed to validate the utility of the implantation protocol of the C-Cl moieties on the PMMA. The analytical results of the X-ray absorption near-edge structure (XANES) analysis also demonstrated the feasibility of the Cl-containing PMMA used as an extraction medium by virtue of the dipole-ion interactions between the highly electronegative C-Cl moieties and the positively charged metal ions.

The fabrication protocol of a dipole-assisted solid phase extraction microchip for the trace metal analysis is presented.

This paper describes a fabrication protocol for a dipole-assisted solid phase extraction (SPE) microchip available for trace metal analysis in water ...

Bioengineering

Solid-Liquid Extraction

Source: Laboratory of Dr. Jay Deiner &#8212; City University of New York
Extraction is a crucial step in most chemical analyses. It entails removing the analyte from its sample matrix and passing it into the phase required for spectroscopic or chromatographic identification and quantification. When the sample is a solid and the required phase for analysis is a liquid, the process is called solid-liquid extraction. A simple and broadly applicable form of solid-liquid extraction entails combining the solid with a solvent in which the analyte is soluble. Through agitation, the analyte partitions into the liquid phase, which may then be separated from the solid through filtration. The choice of solvent must be made based on the solubility of the target analyte, and on the balance of cost, safety, and environmental concerns.

Solid-Liquid Extraction: Principle, Procedure, Applications

Source: Laboratory of Dr. Jay Deiner &#8212; City University of New York
Extraction is a crucial step in most chemical analyses. It entails removing the ...

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Chemistry

Organic Chemistry

Extraction of Biomarkers from Sediments - Accelerated Solvent Extraction

Source: Laboratory of Jeff Salacup&#160;- University of Massachusetts Amherst
The distribution of a group of organic biomarkers called glycerol-dialkyl glycerol-tetraethers (GDGTs), produced by a suite of archaea and bacteria, were found in modern sediments to change in a predictable manner in response to air or water temperature1,2. Therefore, the distribution of these biomarkers in a sequence of sediments of known age can be used to reconstruct the evolution of air and/or water temperature on decadal to millennial timescales (Figure 1). The production of long high-resolution records of past climates, called paleoclimatology, depends on the rapid analysis of hundreds, possibly thousands of samples. Older extraction techniques, such as sonication or Soxhlet, are too slow. However, the newer Accelerated Solvent Extraction technique was designed with efficiency in mind.
<img alt="Figure 1" src="/files/ftp_upload/10097/10097fig1.jpg" /> 
Figure 1. An example of a paleoclimate record showing changes in sea surface temperature (SST) in the eastern Mediterranean Sea during the past ~27,000 years3. This record comprises ~115 samples and is based on the isoprenoidal GDGT-based TEX86 SST proxy.

Accelerated Solvent Extraction of Total Lipid from Sediments

Source: Laboratory of Jeff Salacup&#160;- University of Massachusetts Amherst
The distribution of a group of organic biomarkers called glycerol-dialkyl ...

A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants

Summary

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Extraction and Characterization of Surfactants from Atmospheric Aerosols

A Modified EPA Method 1623 that Uses Tangential Flow Hollow-fiber Ultrafiltration and Heat Dissociation Steps to Detect Waterborne Cryptosporidium and Giardia spp.

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Fabrication of a Dipole-assisted Solid Phase Extraction Microchip for Trace Metal Analysis in Water Samples

Solid-Liquid Extraction

Extraction of Biomarkers from Sediments - Accelerated Solvent Extraction