Name: use of autometallography to localize and semi-quantify silver in cetacean tissues
Uploaded: 2018-10-04T13:30:00
Description: Watch this Scientific Journal Video about Use of Autometallography to Localize and Semi-Quantify Silver in Cetacean Tissues at JoVE.com

We thank the Taiwan Cetacean Stranding Network for sample collection and storage, including the Taiwan Cetacean Society, Taipei; the Cetacean Research Laboratory (Prof. Lien-Siang Chou), the Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei; the National Museum of Natural Science (Dr. Chiou-Ju Yao), Taichung; and the Marine Biology &#38; Cetacean Research Center, National Cheng-Kung University. We also thank the Forestry Bureau, Council of Agriculture, Executive Yuan for their permit.

The study was performed in accordance with international guidelines, and the use of cetacean tissue samples was permitted by the Council of Agriculture of Taiwan (Research Permit 104-07.1-SB-62).
1. Tissue Sample Preparation for ICP-MS Analysis
Note: The liver and kidney tissues were collected from freshly dead and moderately autolyzed stranded cetaceans24, including 6 stranded cetaceans of 4 different species, 1 Grampus griseus (Gg), ...

<ol>
	<li>McGillicuddy, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silver+nanoparticles+in+the+environment:+Sources,+detection+and+ecotoxicology.">Silver nanoparticles in the environment: Sources, detection and ecotoxicology.</a> Science Total Environment. 575, 231-246 (2017).</li><li>Yu, S. J., Yin, Y. G., Liu, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silver+nanoparticles+in+the+environment.">Silver nanoparticles in the environment.</a> Environmental Science: Processes and Impacts. 15 (1), 78-92 (2013).</li><li>Hansen, S. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoproducts-+what+is+actually+available+to+European+consumers?.">Nanoproducts- what is actually available to European consumers?.</a> Environmental Science: Nano. 3 (1), 169-180 (2016).</li><li>Vance, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanotechnology+in+the+real+world:+Redeveloping+the+nanomaterial+consumer+products+inventory.">Nanotechnology in the real world: Redeveloping the nanomaterial consumer products inventory.</a> Beilstein Journal of Nanotechnology. 6, 1769-1780 (2015).</li><li>Farre, M., Gajda-Schrantz, K., Kantiani, L., Barcelo, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ecotoxicity+and+analysis+of+nanomaterials+in+the+aquatic+environment.">Ecotoxicity and analysis of nanomaterials in the aquatic environment.</a> Analytical and Bioanalytical Chemistry. 393 (1), 81-95 (2009).</li><li>Walters, C. R., Pool, E. J., Somerset, V. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ecotoxicity+of+silver+nanomaterials+in+the+aquatic+environment:+a+review+of+literature+and+gaps+in+nano-toxicological+research.">Ecotoxicity of silver nanomaterials in the aquatic environment: a review of literature and gaps in nano-toxicological research.</a> Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances &amp; Environmental Engineering. 49 (13), 1588-1601 (2014).</li><li>Levard, C., Hotze, E. M., Lowry, G. V., Brown, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Environmental+transformations+of+silver+nanoparticles:+impact+on+stability+and+toxicity.">Environmental transformations of silver nanoparticles: impact on stability and toxicity.</a> Environmental Science &amp; Technology. 46 (13), 6900-6914 (2012).</li><li>Massarsky, A., Trudeau, V. L., Moon, T. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+the+environmental+impact+of+nanosilver.">Predicting the environmental impact of nanosilver.</a> Environmental Toxicology and Pharmacology. 38 (3), 861-873 (2014).</li><li>Wang, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toxicity,+bioaccumulation,+and+biotransformation+of+silver+nanoparticles+in+marine+organisms.">Toxicity, bioaccumulation, and biotransformation of silver nanoparticles in marine organisms.</a> Environmental Science and Technology. 48 (23), 13711-13717 (2014).</li><li>Buffet, P. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+marine+mesocosm+study+on+the+environmental+fate+of+silver+nanoparticles+and+toxicity+effects+on+two+endobenthic+species:+the+ragworm+Hediste+diversicolor+and+the+bivalve+mollusc+Scrobicularia+plana.">A marine mesocosm study on the environmental fate of silver nanoparticles and toxicity effects on two endobenthic species: the ragworm Hediste diversicolor and the bivalve mollusc Scrobicularia plana.</a> Science of the Total Environment. 470, 1151-1159 (2014).</li><li>Chen, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baseline+metal+concentrations+in+sediments+and+fish,+and+the+determination+of+bioindicators+in+the+subtropical+Chi-ku+Lagoon,+S+W+Taiwan.">Baseline metal concentrations in sediments and fish, and the determination of bioindicators in the subtropical Chi-ku Lagoon, S W Taiwan.</a> Marine Pollution Bulletin. 44 (7), 703-714 (2002).</li><li>Li, W. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigation+of+silver+(Ag)+deposition+in+tissues+from+stranded+cetaceans+by+autometallography+(AMG).">Investigation of silver (Ag) deposition in tissues from stranded cetaceans by autometallography (AMG).</a> Environmental Pollution. , 534-545 (2018).</li><li>Chen, M. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+concentrations+of+four+Taiwanese+toothed+cetaceans+indicating+the+silver+and+cadmium+pollution+in+the+western+Pacific+Ocean.">Tissue concentrations of four Taiwanese toothed cetaceans indicating the silver and cadmium pollution in the western Pacific Ocean.</a> Marine Pollution Bulletin. 124 (2), 993-1000 (2017).</li><li>Li, W. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunotoxicity+of+silver+nanoparticles+(AgNPs)+on+the+leukocytes+of+common+bottlenose+dolphins+(Tursiops+truncatus).">Immunotoxicity of silver nanoparticles (AgNPs) on the leukocytes of common bottlenose dolphins (Tursiops truncatus).</a> Scientific Reports. , (2018).</li><li>Bornhorst, J. A., Hunt, J. W., Urry, F. M., McMillin, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+sample+preservation+methods+for+clinical+trace+element+analysis+by+inductively+coupled+plasma+mass+spectrometry.">Comparison of sample preservation methods for clinical trace element analysis by inductively coupled plasma mass spectrometry.</a> American Journal of Clinical Pathology. 123 (4), 578-583 (2005).</li><li>Bonta, M., Torok, S., Hegedus, B., Dome, B., Limbeck, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+sample+preparation+strategies+for+biological+tissues+and+subsequent+trace+element+analysis+using+LA-ICP-MS.">A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.</a> Analytical and Bioanalytical Chemistry. 409 (7), 1805-1814 (2017).</li><li>Bischoff, K., Lamm, C., Erb, H. N., Hillebrandt, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effects+of+formalin+fixation+and+tissue+embedding+of+bovine+liver+on+copper,+iron,+and+zinc+analysis.">The effects of formalin fixation and tissue embedding of bovine liver on copper, iron, and zinc analysis.</a> Journal of Veterinary Diagnostic Investigation. 20 (2), 220-224 (2008).</li><li>Miller, D. L., Yu, I. J., Genter, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+Autometallography+in+Studies+of+Nanosilver+Distribution+and+Toxicity.">Use of Autometallography in Studies of Nanosilver Distribution and Toxicity.</a> International Journal of Toxicology. 35 (1), 47-51 (2016).</li><li>Anderson, D. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+particle+size+on+persistence+and+clearance+of+aerosolized+silver+nanoparticles+in+the+rat+lung.">Influence of particle size on persistence and clearance of aerosolized silver nanoparticles in the rat lung.</a> Toxicological Sciences. 144 (2), 366-381 (2015).</li><li>Kim, W. Y., Kim, J., Park, J. D., Ryu, H. Y., Yu, I. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histological+study+of+gender+differences+in+accumulation+of+silver+nanoparticles+in+kidneys+of+Fischer+344+rats.">Histological study of gender differences in accumulation of silver nanoparticles in kidneys of Fischer 344 rats.</a> Journal of Toxicology and Environmental Health, Part A. 72 (21-22), 1279-1284 (2009).</li><li>Danscher, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+autometallography+to+heavy+metal+toxicology.">Applications of autometallography to heavy metal toxicology.</a> Pharmacology Toxicology. 68 (6), 414-423 (1991).</li><li>Deroulers, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+huge+pathology+images+with+open+source+software.">Analyzing huge pathology images with open source software.</a> Diagnostic Pathology. 8, 92 (2013).</li><li>Shu, J., Dolman, G. E., Duan, J., Qiu, G., Ilyas, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+colour+models:+an+automated+digital+image+analysis+method+for+quantification+of+histological+biomarkers.">Statistical colour models: an automated digital image analysis method for quantification of histological biomarkers.</a> BioMedical Engineering Online. 15, 46 (2016).</li><li>Geraci, J. R., Lounsbury, V. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specimen+and+data+collection.">Specimen and data collection.</a> Marine mammals ashore: a field guide for strandings. , 167-230 (2005).</li><li>Shih, C. -. C., Liu, L. -. L., Chen, M. -. H., Wang, W. -. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Investigation of heavy metal bioaccumulation in dolphins from the coastal waters off Taiwan. , (2001).</li><li>Liang, C. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+relationship+between+the+striatal+dopamine+transporter+and+novelty+seeking+and+cognitive+flexibility+in+opioid+dependence.">The relationship between the striatal dopamine transporter and novelty seeking and cognitive flexibility in opioid dependence.</a> Progress in Neuro-Psychopharmacology and Biological Psychiatry. 74, 36-42 (2017).</li><li>Spiess, A. N., Neumeyer, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+evaluation+of+R2+as+an+inadequate+measure+for+nonlinear+models+in+pharmacological+and+biochemical+research:+a+Monte+Carlo+approach.">An evaluation of R2 as an inadequate measure for nonlinear models in pharmacological and biochemical research: a Monte Carlo approach.</a> BMC Pharmacology. 10, 6 (2010).</li><li>Stoltenberg, M., Danscher, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histochemical+differentiation+of+autometallographically+traceable+metals+(Au,+Ag,+Hg,+Bi,+Zn):+protocols+for+chemical+removal+of+separate+autometallographic+metal+clusters+in+Epon+sections.">Histochemical differentiation of autometallographically traceable metals (Au, Ag, Hg, Bi, Zn): protocols for chemical removal of separate autometallographic metal clusters in Epon sections.</a> Histochemical Journal. 32 (11), 645-652 (2000).</li><li>Dimitriadis, V. K., Domouhtsidou, G. P., Raftopoulou, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Localization+of+Hg+and+Pb+in+the+palps,+the+digestive+gland+and+the+gills+in+Mytilus+galloprovincialis+(L.)+using+autometallography+and+X-ray+microanalysis.">Localization of Hg and Pb in the palps, the digestive gland and the gills in Mytilus galloprovincialis (L.) using autometallography and X-ray microanalysis.</a> Environmental Pollution. 125 (3), 345-353 (2003).</li><li>Loumbourdis, N. S., Danscher, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Autometallographic+tracing+of+mercury+in+frog+liver.">Autometallographic tracing of mercury in frog liver.</a> Environmental Pollution. 129 (2), 299-304 (2004).</li><li>Stoltenberg, M., Larsen, A., Kemp, K., Bloch, D., Weihe, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Autometallographic+tracing+of+mercury+in+pilot+whale+tissues+in+the+Faroe+Islands.">Autometallographic tracing of mercury in pilot whale tissues in the Faroe Islands.</a> International Journal of Circumpolar Health. 62 (2), 182-189 (2003).</li></ol>

The purpose of the article study is to establish an adjuvant method to evaluate the Ag distribution at suborgan levels and to estimate Ag concentrations in cetacean tissues. The current protocols include 1) Determination of Ag concentrations in cetacean tissues by ICP-MS, 2) AMG analysis of pair-matched tissue samples with known Ag concentrations, 3) Establishment of the regression model (CHAA) for estimating the Ag concentrations by AMG positive values, 4) Evaluation of the accuracy and precision of CHAA, and 5) Estimat...

Silver nanoparticles (AgNPs) have been extensively used in commercial products, including textiles, cosmetics, and health care items, due to their great antimicrobial effects1,2. Therefore, the production of AgNPs and the number of AgNP-containing products are increased over time3,4. However, AgNPs may be released into the environment and accumulate in the ocean5,6. They have become the major source of Ag contamination, and the public awareness of the environmental toxicity of Ag is increasing.
The status of AgNPs and Ag in the marine environment is complicated and constantly changing. Previous studies have indicated that AgNPs can remain as particles, aggregate, dissolve, react with different chemical species, or be regenerated from Ag+ ions7,8. Several types of Ag compounds, such as AgCl, have been found in marine sediments, where they can be ingested by benthic organisms and enter the food chain9,10. According to a previous study conducted in the Chi-ku Lagoon area along the southwestern coast of Taiwan, the Ag concentrations of marine sediments are extremely low and similar to the crustal abundance, and those of fish liver tissue are usually below the detection limit (&#60; 0.025 &#956;g/g wet/wet)11. However, previous studies conducted in different countries have demonstrated relatively high Ag concentrations in the livers of cetaceans12,13. The Ag concentration in the livers of cetaceans is age-dependent, suggesting that the source of Ag in their bodies is most likely their prey12. These findings further suggest the biomagnification of Ag in animals at higher trophic levels. Cetaceans, as the apex predators in the ocean, may have suffered negative health impacts caused by Ag/Ag compounds12,13,14. Most importantly, like cetaceans, humans are mammals, and the negative health impacts caused by Ag/Ag compounds in cetaceans may also occur in humans. In other words, cetaceans could be sentinel animals for the health of marine environment and humans. Therefore, the health effects, the tissue distribution, and concentration of Ag in cetaceans are of great concern.
Although the concentrations of Ag/Ag compounds in cetacean tissues can be measured by inductively coupled plasma mass spectroscopy (ICP-MS), the use of ICP-MS is limited by its high capital cost (instrument and maintenance) and the requirements for tissue storage/preparation12,15. In addition, it is usually difficult to collect comprehensive tissue samples in all investigations of stranded cetacean cases due to logistical difficulties, a shortage of manpower, and a lack of related resources12. The frozen tissue samples for ICP-MS analysis are not easily stored because of limited refrigeration space, and frozen tissue samples may be discarded due to broken refrigeration equipment12. These aforementioned obstacles hamper investigations of contamination levels in cetacean tissues by ICP-MS analysis using frozen tissue samples. In contrast, formalin fixed tissue samples are relatively easy to collect during the necropsy of dead-stranded cetaceans. Therefore, it is necessary to develop an easy to use and inexpensive method to detect/measure the heavy metals in cetacean tissues by using formalin fixed tissue samples.
Although the suborgan distributions and concentrations of alkali and alkaline earth metals may be altered during the formalin-fixed, paraffin-embedded (FFPE) process, only lesser effects on transition metals, such as Ag, have been noted16. Hence, FFPE tissue has been considered as an ideal sample resource for metal localization and measurements16,17. Autometallography (AMG), a histochemical process, can amplify heavy metals as variably sized golden yellow to black AMG positive signals on FFPE tissue sections, and these amplified heavy metals can be visualized under light microscopy18,19,20,21. Hence, the AMG method provides information on the suborgan distributions of heavy metals. It can provide important additional information for studying the metabolic pathways of heavy metals in biological systems because ICP-MS can only measure the concentration of heavy metals at the organ level18. Furthermore, digital image analysis software, such as ImageJ, has been applied to the quantitative analysis of histological tissue sections22,23. The variably-sized golden yellow to black AMG positive signals of FFPE tissue sections can be quantified and used to estimate the concentrations of heavy metals. Although the absolute Ag concentration cannot be directly determined by the AMG method with image quantitative analysis, it can be estimated by a regression model based on the data obtained from the image quantitative analysis and ICP-MS, which is named cetacean histological Ag assay (CHAA). Considering the difficulties in measuring Ag concentrations by ICP-MS analysis in most stranded cetaceans, CHAA is a valuable adjuvant method to estimate Ag concentrations in cetacean tissues, which cannot be determined by ICP-MS analysis due to the lack of frozen tissue samples. This paper describes the protocol of a histochemical technique (AMG method) for localizing Ag at the suborgan level and an assay named CHAA to estimate the Ag concentrations in the liver and kidney tissues of cetaceans.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/58232/58232fig1.jpg" /> 
Figure 1: Flowchart depicting the establishment and application of cetacean histological Ag assay (CHAA) for estimating Ag concentrations. CHAA = cetacean histological Ag assay, FFPE = Formalin-fixed, paraffin-embedded, ICP-MS = inductively coupled plasma mass spectroscopy. <a href="https://www.jove.com/files/ftp_upload/58232/58232fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table>
	<tbody>
		<tr>
			<td>HQ Silver enhancement kit</td>
			<td>Nanoprobes</td>
			<td>#2012</td>
			<td></td>
		</tr>
		<tr>
			<td>Surgipath Paraplast</td>
			<td>Leica Biosystems</td>
			<td>39601006</td>
			<td>Paraffin</td>
		</tr>
		<tr>
			<td>100% Ethanol</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>4026</td>
			<td></td>
		</tr>
		<tr>
			<td>Non-Xylene</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>4328</td>
			<td></td>
		</tr>
		<tr>
			<td>Silane coated slide</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>511614</td>
			<td></td>
		</tr>
		<tr>
			<td>Cover glass (25 x 50 mm)</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>24501</td>
			<td></td>
		</tr>
		<tr>
			<td>Malinol</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>20092</td>
			<td></td>
		</tr>
		<tr>
			<td>GM Haematoxylin Staining</td>
			<td>Muto Pure Chemical Co., Ltd</td>
			<td>3008-1</td>
			<td></td>
		</tr>
		<tr>
			<td>10% neutral buffered formalin solution</td>
			<td>Chin I Pao Co., Ltd</td>
			<td>---</td>
			<td></td>
		</tr>
		<tr>
			<td>Tip (1000 &#956;L)</td>
			<td>MDBio, Inc.</td>
			<td>1000</td>
			<td></td>
		</tr>
		<tr>
			<td>PIPETMAN Classic P1000</td>
			<td>Gilson, Inc.</td>
			<td>F123602</td>
			<td></td>
		</tr>
		<tr>
			<td>15 ml Centrifuge Tube</td>
			<td>GeneDireX, Inc.</td>
			<td>PC115-0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Dogfish liver</td>
			<td>National Research Council of Canada</td>
			<td>DOLT-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Dogfish muscle</td>
			<td>National Research Council of Canada</td>
			<td>DORM-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Inductively coupled plasma mass spectrometry (ICP-MS)</td>
			<td>PerkinElmer Inc.</td>
			<td>PE-SCIEX ELAN 6100 DRC</td>
			<td></td>
		</tr>
		<tr>
			<td>FreeZone 6 liter freeze dry system</td>
			<td>Labconco</td>
			<td>7752030</td>
			<td>For freeze drying</td>
		</tr>
		<tr>
			<td>BRAND&#174; SILBERBRAND volumetric flask</td>
			<td>Merck</td>
			<td>Z326283</td>
			<td></td>
		</tr>
		<tr>
			<td>30 mL standard vial, flat interior with 33 mm closure</td>
			<td>Savillex Corporation</td>
			<td>200-030-12</td>
			<td>For diagestion</td>
		</tr>
		<tr>
			<td>Nitric acid, superpur&#174;, 65.0%</td>
			<td>Merck</td>
			<td>1.00441</td>
			<td>For diagestion</td>
		</tr>
		<tr>
			<td>Hot Plate/Stirrers</td>
			<td>Corning&#174;</td>
			<td>PC-220</td>
			<td>For diagestion</td>
		</tr>
		<tr>
			<td>High Shear lab mixer</td>
			<td>Silverson</td>
			<td>SL2T</td>
			<td>For homogenization</td>
		</tr>
		<tr>
			<td>Sterile polypropylene sample jar (250mL)</td>
			<td>Thermo Scientific&#8482;</td>
			<td>6186L05</td>
			<td>For homogenization</td>
		</tr>
		<tr>
			<td>Digital camera</td>
			<td>Nikon Corporation</td>
			<td>DS-Fi2</td>
			<td></td>
		</tr>
		<tr>
			<td>Light microscope</td>
			<td>Nikon Corporation</td>
			<td>ECLIPSE Ni-U</td>
			<td></td>
		</tr>
		<tr>
			<td>Shandon&#8482; Finesse&#8482; 325 manual microtome</td>
			<td>Thermo Scientific&#8482;</td>
			<td>A78100001H</td>
			<td></td>
		</tr>
		<tr>
			<td>Accu-Cut&#174; SRM&#8482; 200 rotary microtome</td>
			<td>Sakura</td>
			<td>1429</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtome blade S35</td>
			<td>FEATHER&#174;</td>
			<td>207500000</td>
			<td></td>
		</tr>
		<tr>
			<td>Slide staining dish and cover</td>
			<td>Brain Research Laboratories</td>
			<td>#3215</td>
			<td></td>
		</tr>
		<tr>
			<td>Steel staining rack</td>
			<td>Brain Research Laboratories</td>
			<td>#3003</td>
			<td></td>
		</tr>
		<tr>
			<td>Shandon embedding center</td>
			<td>Thermo Scientific&#8482;</td>
			<td>S-EC</td>
			<td></td>
		</tr>
		<tr>
			<td>Shandon Citadel&#174; tissue processor</td>
			<td>Thermo Scientific&#8482;</td>
			<td>69800003</td>
			<td></td>
		</tr>
		<tr>
			<td>Slide warmer</td>
			<td>Lab-Line Instruments</td>
			<td>26005</td>
			<td></td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td>Shandon Capshaw</td>
			<td>3964</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Merck</td>
			<td>1541-070</td>
			<td></td>
		</tr>
		<tr>
			<td>Prism 6.01 for windows</td>
			<td>GraphPad Software</td>
			<td></td>
			<td>Statistic software</td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>National Institutes of Health</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Stainless steel tissue embedding mould</td>
			<td>Shenyang Roundfin Trade Co., Ltd</td>
			<td>RD-TBM003</td>
			<td>For paraffin emedding</td>
		</tr>
	</tbody>
</table>

use of autometallography to localize and semi-quantify silver in cetacean tissues

Silver nanoparticles (AgNPs) have been extensively used in commercial products, including textiles, cosmetics, and health care items, due to their strong antimicrobial effects. They also may be released into the environment and accumulate in the ocean. Therefore, AgNPs are the major source of Ag contamination, and public awareness of the environmental toxicity of Ag is increasing. Previous studies have demonstrated the bioaccumulation (in producers) and magnification (in consumers/predators) of Ag. Cetaceans, as the apex predators of ocean, may have been negatively affected by the Ag/Ag compounds. Although the concentrations of Ag/Ag compounds in cetacean tissues can be measured by inductively coupled plasma mass spectroscopy (ICP-MS), the use of ICP-MS is limited by its high capital cost and the requirement for tissue storage/preparation. Therefore, an autometallography (AMG) method with an image quantitative analysis by using formalin-fixed, paraffin-embedded (FFPE) tissue may be an adjuvant method to localize Ag distribution at the suborgan level and estimate the Ag concentration in cetacean tissues. The AMG positive signals are mainly brown to black granules of various sizes in the cytoplasm of proximal renal tubular epithelium, hepatocytes, and Kupffer cells. Occasionally, some amorphous golden yellow to brown AMG positive signals are noted in the lumen and basement membrane of some proximal renal tubules. The assay for estimating the Ag concentration is named the Cetacean Histological Ag Assay (CHAA), which is a regression model established by the data from image quantitative analysis of the AMG method and ICP-MS. The use of AMG with CHAA to localize and semi-quantify heavy metals provides a convenient methodology for spatio-temporal and cross-species studies.

Representative images of the AMG positive signals in the cetacean liver and kidney tissues are shown in Figure 5. The AMG positive signals include variably-sized brown to black granules of various sizes in the cytoplasm of proximal renal tubular epithelium, hepatocytes, and Kupffer cells. Occasionally, amorphous golden yellow to brown AMG positive signals are noted in the lumen and basement membrane of some proximal renal tubules. There is a positive correlat...

Watch this Scientific Journal Video about Use of Autometallography to Localize and Semi-Quantify Silver in Cetacean Tissues at JoVE.com

Use of Autometallography to Localize and Semi-Quantify Silver in Cetacean Tissues

A protocol is presented to localize Ag in cetacean liver and kidney tissues by autometallography. Furthermore, a new assay, named the cetacean histological Ag assay (CHAA) is developed to estimate the Ag concentrations in those tissues.

Silver nanoparticles (AgNPs) have been extensively used in commercial products, including textiles, cosmetics, and health care items, due to their strong ...

This method can help answer key questions in the field of environmental toxicology about sub-organ distributions and concentration of heavy metals within biological systems. The main advantage of this technique is that AMG is an easy to use and inexpensive methodology, that is a valuable adjuvant for investigating heavy metals in tissues. We use the tissues from dolphins and whales to demonstrate the protocol.However, we believe the protocol could be used in a variety of animal species. Demonstrating the procedure with Wen-Ta Li will be Shun Theng, a clinician from our institute. Begin by collecting pair-matched liver and kidney tissues for AMG analysis from a stranded cetacean, and fixing the tissue in 10 times the volume of 10%neutral buffered formalin for 24 to 48 hours.Next, use disposable stainless steel microtome blades to trim the formalin-fixed liver and kidney tissues into two-centimeter by one-centimeter, three-millimeter sections, and place both liver and kidney sections from the same individual into the same labeled cassettes. Dehydrate the sections in a tissue processor through a series of graded ethanol and xylene immersions, followed by one-hour and two-hour paraffin immersions. After the two-hour paraffin immersion, transfer the tissues to the bottoms of steel histology molds and embed the dehydrated tissue samples with fresh melted paraffin.Chill the formalin-fixed, paraffin-embedded tissue blocks on a cold plate, until the paraffin solidifies, and trim each block at the microtome until the tissue surface is exposed. Chill the samples at minus 20 degrees Celsius for 10 minutes, and obtain five-micrometer tissue sections on the microtome. Using tweezers and brushes, lift the ribbons of tissue section as they are acquired, and float them on the surface of a 45 degree Celsius double-distilled water bath, until they can be separated, and place onto individual microscope slides.Then, place the slides on a slide warmer for one hour, at 60 degrees Celsius. Then, place the slides in slide racks, and de-paraffinize the sections in three different staining dishes containing 200 to 250 milliliters of pure non-xylene for eight-five-and three-minute incubations. Hydrate the de-parrafinized samples in different staining dishes of graded ethanol solutions, followed by rinsing in double-distilled water.Rinse the sections one time in PBS supplemented with 5%Triton X 100, several times in PBS alone, and one time in fresh double-distilled water for 30 seconds per wash. After the last wash, label each sample with 300 microliters of mixed silver enhancement kit solution, for no more than 15 minutes in the dark at room temperature. At the end of the incubation, wash the slides with double-distilled water, and counter-stain the sections in 300 microliters of hematoxylin per slide, for 10 seconds.Wash the slides with running tap water. Dry them and mount the sections with mounting medium. Then, capture 10 random histological images of each tissue section, under the 40X objective of a light microscope.To analyze the autometallography, or AMG, positivity of the samples, open the images in an appropriate image analysis software program, and select image, type, and RGB stack, to split the first image into the red, blue, and green color channels. In the blue channel, select image, adjust, and threshold, to measure the percentage of the area with AMG-positive signals in each image, manually adjusting the cut-off value for the threshold of each image based on the presence of false-positive areas in the nuclei, or red blood cells. Click analyze, and set measurements, and check the area fraction, to specify that the area fraction is recorded.Click analyze, and measure, to display the positive percent area of each histological image percent area column of the result window. To evaluate the correlation between the results of inductively-coupled plasma mass spectroscopy and AMG-positive values, open the appropriate graphing software. Create a new project file, and select XY and correlation.Input the results of the inductively-coupled plasma mass spectroscopy and AMG analyses, and select analysis, and correlation, to analyze the strength of association between the results of the analysis by Pearson correlation analysis. In the parameters, non-linear regression window, select a different regression model on the fit page, and select the comparison methods on the compare page. Include the extra sum of squares F test, and Akaike's Information Criterion.According to the results of the comparison methods, select a relatively appropriate regression model in the cetacean histological silver assay, and use the assay to estimate the silver concentrations of the cetacean liver and kidney tissues, with unknown silver concentrations. AMG-positive signals include variably-sized, brown to black granules in the cytoplasm of hepatocytes and Kupffer cells, and occasional amorphous, golden yellow to brown AMG-positive signals in the lumen and basement membrane of some proximal renal tubules. There is a positive correlation between the results of inductively-coupled plasma mass spectroscopy and AMG-positivity values in the analyzed liver and kidney tissues, with a preferred linear regression through the origin, according to the extra sum of squares F test, and Akaike's Information Criterion.While attempting this procedure, it's important to remember that the AMG method is an adjuvant method, and must be used with other specific method, such as ICPMS, for monitoring the actual composition of heavy metals in tissues.

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Research

JoVE Journal

Environment

Optimize Flue Gas Settings to Promote Microalgae Growth in Photobioreactors via Computer Simulations

Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently than plants3, but also synthesize advanced biofuels2-4. Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth5. On the other hand, the high concentrations of CO2 in industrial exhaust gases have adverse effects on algal physiology. Consequently, both cultivation conditions (such as nutrients and light) and the control of the flue gas flow into the photo-bioreactors are important to develop an efficient &ldquo;flue gas to algae&rdquo; system. Researchers have proposed different photobioreactor configurations4,6 and cultivation strategies7,8 with flue gas. Here, we present a protocol that demonstrates how to use models to predict the microalgal growth in response to flue gas settings. We perform both experimental illustration and model simulations to determine the favorable conditions for algal growth with flue gas. We develop a Monod-based model coupled with mass transfer and light intensity equations to simulate the microalgal growth in a homogenous photo-bioreactor. The model simulation compares algal growth and flue gas consumptions under different flue-gas settings. The model illustrates: 1) how algal growth is influenced by different volumetric mass transfer coefficients of CO2; 2) how we can find optimal CO2 concentration for algal growth via the dynamic optimization approach (DOA); 3) how we can design a rectangular on-off flue gas pulse to promote algal biomass growth and to reduce the usage of flue gas. On the experimental side, we present a protocol for growing Chlorella under the flue gas (generated by natural gas combustion). The experimental results qualitatively validate the model predictions that the high frequency flue gas pulses can significantly improve algal cultivation.

Flue gas from power plants is a cheap CO2 source for algal growth. We have built prototype &#34;flue gas to algal cultivation&#34; systems and described how to scale up the algal cultivation process. We have demonstrated the use of a mass-transfer bio-reaction model to simulate and to design the optimal operation of flue gas for the growth of Chlorella sp. in algal photo-bioreactors.

Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently ...

Technique for Studying Arthropod and Microbial Communities within Tree Tissues

Phloem tissues of pine are habitats for many thousands of organisms. Arthropods and microbes use phloem and cambium tissues to seek mates, lay eggs, rear young, feed, or hide from natural enemies or harsh environmental conditions outside of the tree. Organisms that persist within the phloem habitat are difficult to observe given their location under bark. We provide a technique to preserve intact phloem and prepare it for experimentation with invertebrates and microorganisms. The apparatus is called a &#8216;phloem sandwich&#8217; and allows for the introduction and observation of arthropods, microbes, and other organisms. This technique has resulted in a better understanding of the feeding behaviors, life-history traits, reproduction, development, and interactions of organisms within tree phloem. The strengths of this technique include the use of inexpensive materials, variability in sandwich size, flexibility to re-open the sandwich or introduce multiple organisms through drilled holes, and the preservation and maintenance of phloem integrity. The phloem sandwich is an excellent educational tool for scientific discovery in both K-12 science courses and university research laboratories.

We provide a technique to preserve intact tree phloem and prepare it for observation. We create an apparatus called a phloem sandwich that allows for the introduction and observation of arthropods, microbes, and other organisms that inhabit phloem tissues.

Phloem tissues of pine are habitats for many thousands of organisms.  Arthropods and microbes use phloem and cambium tissues to seek mates, lay eggs, rear ...

Transient Gene Expression in Tobacco using Gibson Assembly and the Gene Gun

In order to target a single protein to multiple subcellular organelles, plants typically duplicate the relevant genes, and express each gene separately using complex regulatory strategies including differential promoters and/or signal sequences. Metabolic engineers and synthetic biologists interested in targeting enzymes to a particular organelle are faced with a challenge: For a protein that is to be localized to more than one organelle, the engineer must clone the same gene multiple times. This work presents a solution to this strategy: harnessing alternative splicing of mRNA. This technology takes advantage of established chloroplast and peroxisome targeting sequences and combines them into a single mRNA that is alternatively spliced. Some splice variants are sent to the chloroplast, some to the peroxisome, and some to the cytosol. Here the system is designed for multiple-organelle targeting with alternative splicing. In this work, GFP was expected to be expressed in the chloroplast, cytosol, and peroxisome by a series of rationally designed 5&#8217; mRNA tags. These tags have the potential to reduce the amount of cloning required when heterologous genes need to be expressed in multiple subcellular organelles. The constructs were designed in previous work11, and were cloned using Gibson assembly, a ligation independent cloning method that does not require restriction enzymes. The resultant plasmids were introduced into Nicotiana benthamiana epidermal leaf cells with a modified Gene Gun protocol. Finally, transformed leaves were observed with confocal microscopy.

This work describes a novel method for selectively targeting subcellular organelles in plants, assayed using the BioRad Gene Gun.

In order to target a single protein to multiple subcellular organelles, plants typically duplicate the relevant genes, and express each gene separately ...

A Fish-feeding Laboratory Bioassay to Assess the Antipredatory Activity of Secondary Metabolites from the Tissues of Marine Organisms

Marine chemical ecology is a young discipline, having emerged from the collaboration of natural products chemists and marine ecologists in the 1980s with the goal of examining the ecological functions of secondary metabolites from the tissues of marine organisms. The result has been a progression of protocols that have increasingly refined the ecological relevance of the experimental approach. Here we present the most up-to-date version of a fish-feeding laboratory bioassay that enables investigators to assess the antipredatory activity of secondary metabolites from the tissues of marine organisms. Organic metabolites of all polarities are exhaustively extracted from the tissue of the target organism and reconstituted at natural concentrations in a nutritionally appropriate food matrix. Experimental food pellets are presented to a generalist predator in laboratory feeding assays to assess the antipredatory activity of the extract. The procedure described herein uses the bluehead, Thalassoma bifasciatum, to test the palatability of Caribbean marine invertebrates; however, the design may be readily adapted to other systems. Results obtained using this laboratory assay are an important prelude to field experiments that rely on the feeding responses of a full complement of potential predators. Additionally, this bioassay can be used to direct the isolation of feeding-deterrent metabolites through bioassay-guided fractionation. This feeding bioassay has advanced our understanding of the factors that control the distribution and abundance of marine invertebrates on Caribbean coral reefs and may inform investigations in diverse fields of inquiry, including pharmacology, biotechnology, and evolutionary ecology.

This bioassay employs a model predatory fish to assess the presence of feeding-deterrent metabolites from organic extracts of the tissues of marine organisms at natural concentrations using a nutritionally comparable food matrix.

Marine chemical ecology is a young discipline, having emerged from the collaboration of natural products chemists and marine ecologists in the 1980s with ...

The Use of High-resolution Infrared Thermography (HRIT) for the Study of Ice Nucleation and Ice Propagation in Plants

Freezing events that occur when plants are actively growing can be a lethal event, particularly if the plant has no freezing tolerance. Such frost events often have devastating effects on agricultural production and can also play an important role in shaping community structure in natural populations of plants, especially in alpine, sub-arctic, and arctic ecosystems. Therefore, a better understanding of the freezing process in plants can play an important role in the development of methods of frost protection and understanding mechanisms of freeze avoidance. Here, we describe a protocol to visualize the freezing process in plants using high-resolution infrared thermography (HRIT). The use of this technology allows one to determine the primary sites of ice formation in plants, how ice propagates, and the presence of ice barriers. Furthermore, it allows one to examine the role of extrinsic and intrinsic nucleators in determining the temperature at which plants freeze and evaluate the ability of various compounds to either affect the freezing process or increase freezing tolerance. The use of HRIT allows one to visualize the many adaptations that have evolved in plants, which directly or indirectly impact the freezing process and ultimately enables plants to survive frost events.

The Use of High-resolution Infrared Thermography HRIT for the Study of Ice Nucleation and Ice Propagation in Plants

Here we present a protocol that allows one to visualize sites of ice formation and avenues of ice propagation in plants utilizing high resolution infrared thermography (HRIT).

Freezing events that occur when plants are actively growing can be a lethal event, particularly if the plant has no freezing tolerance. Such frost events ...

The Use of an Automated System (GreenFeed) to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals

Ruminant animals (domesticated or wild) emit methane (CH4) through enteric fermentation in their digestive tract and from decomposition of manure during storage. These processes are the major sources of greenhouse gas (GHG) emissions from animal production systems. Techniques for measuring enteric CH4 vary from direct measurements (respiration chambers, which are highly accurate, but with limited applicability) to various indirect methods (sniffers, laser technology, which are practical, but with variable accuracy). The sulfur hexafluoride (SF6)&#160;tracer gas method is commonly used to measure enteric CH4 production by animal scientists and more recently, application of an Automated Head-Chamber System (AHCS) (GreenFeed, C-Lock, Inc., Rapid City, SD), which is the focus of this experiment, has been growing. AHCS is an automated system to monitor CH4 and carbon dioxide (CO2) mass fluxes from the breath of ruminant animals. In a typical AHCS operation, small quantities of baiting feed are dispensed to individual animals to lure them to AHCS multiple times daily. As the animal visits AHCS, a fan system pulls air past the animal&#8217;s muzzle into an intake manifold, and through an air collection pipe where continuous airflow rates are measured. A sub-sample of air is pumped out of the pipe into non-dispersive infra-red sensors for continuous measurement of CH4 and CO2 concentrations. Field comparisons of AHCS to respiration chambers or SF6 have demonstrated that AHCS produces repeatable and accurate CH4 emission results, provided that animal visits to AHCS are sufficient so emission estimates are representative of the diurnal rhythm of rumen gas production. Here, we demonstrate the use of AHCS to measure CO2 and CH4 fluxes from dairy cows given a control diet or a diet supplemented with technical-grade cashew nut shell liquid.

The Use of an Automated System GreenFeed to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals

Accuracy and precision of the techniques used to measure methane emissions from ruminant animals are critically important for the success of greenhouse gas mitigation efforts. This manuscript describes the principles and operation of an automated system to monitor methane and carbon dioxide mass fluxes from the breath of ruminant animals.

Ruminant animals (domesticated or wild) emit methane (CH4) through enteric fermentation in their digestive tract and from decomposition of manure during ...

Use of a Battery of Chemical and Ecotoxicological Methods for the Assessment of the Efficacy of Wastewater Treatment Processes to Remove Estrogenic Potency

Endocrine Disrupting Compounds pose a substantial risk to the aquatic environment. Ethinylestradiol (EE2) and estrone (E1) have recently been included in a watch list of environmental pollutants under the European Water Framework Directive. Municipal wastewater treatment plants are major contributors to the estrogenic potency of surface waters. Much of the estrogenic potency of wastewater treatment plant (WWTP) effluents can be attributed to the discharge of steroid estrogens including estradiol (E2), EE2 and E1 due to incomplete removal of these substances at the treatment plant. An evaluation of the efficacy of wastewater treatment processes requires the quantitative determination of individual substances most often undertaken using chemical analysis methods. Most frequently used methods include Gas Chromatography-Mass Spectrometry (GCMS/MS) or Liquid Chromatography-Mass Spectrometry (LCMS/MS) using multiple reaction monitoring (MRM). Although very useful for regulatory purposes, targeted chemical analysis can only provide data on the compounds (and specific metabolites) monitored. Ecotoxicology methods additionally ensure that any by-products produced or unknown estrogenic compounds present are also assessed via measurement of their biological activity. A number of in vitro bioassays including the Yeast Estrogen Screen (YES) are available to measure the estrogenic activity of wastewater samples. Chemical analysis in conjunction with in vivo and in vitro bioassays provides a useful toolbox for assessment of the efficacy and suitability of wastewater treatment processes with respect to estrogenic endocrine disrupting compounds. This paper utilizes a battery of chemical and ecotoxicology tests to assess conventional, advanced and emerging wastewater treatment processes in laboratory and field studies.

Endocrine Disrupting Compounds (EDC) pose a substantial risk to the aquatic environment. Municipal wastewater treatment plants are major contributors to the estrogenic potency of surface waters. The methodology provided in this paper allows for an assessment of the efficacy and suitability of wastewater treatment processes with respect to EDC removal.

Endocrine Disrupting Compounds pose a substantial risk to the aquatic environment. Ethinylestradiol (EE2) and estrone (E1) have recently been included in ...

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes &#8804;4 L or &gt;4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m3) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

We describe a protocol for filtration of water samples with a filter cartridge and extraction of environmental DNA (eDNA) without having to cut open the housing to remove the filter. This protocol is developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies ...

The Calibration and Use of Capacitance Sensors to Monitor Stem Water Content in Trees

Water transport and storage through the soil-plant-atmosphere continuum is critical to the terrestrial water cycle, and has become a major research focus area. Biomass capacitance plays an integral role in the avoidance of hydraulic impairment to transpiration. However, high temporal resolution measurements of dynamic changes in the hydraulic capacitance of large trees are rare. Here, we present procedures for the calibration and use of capacitance sensors, typically used to monitor soil water content, to measure the volumetric water content in trees in the field. Frequency domain reflectometry-style observations are sensitive to the density of the media being studied. Therefore, it is necessary to perform species-specific calibrations to convert from the sensor-reported values of dielectric permittivity to volumetric water content. Calibration is performed on a harvested branch or stem cut into segments that are dried or re-hydrated to produce a full range of water contents used to generate a best-fit regression with sensor observations. Sensors are inserted into calibration segments or installed in trees after pre-drilling holes to a tolerance fit using a fabricated template to ensure proper drill alignment. Special care is taken to ensure that sensor tines make good contact with the surrounding media, while allowing them to be inserted without excessive force. Volumetric water content dynamics observed via the presented methodology align with sap flow measurements recorded using thermal dissipation techniques and environmental forcing data. Biomass water content data can be used to observe the onset of water stress, drought response and recovery, and has the potential to be applied to the calibration and evaluation of new plant-level hydrodynamics models, as well as to the partitioning of remotely sensed moisture products into above- and belowground components.

The hydraulic capacitance of biomass is a key component of the vegetation water budget, which serves as a buffer against short and long-term drought stresses. Here, we present a protocol for the calibration and use of soil moisture capacitance sensors to monitor water content in the stems of large trees.

Water transport and storage through the soil-plant-atmosphere continuum is critical to the terrestrial water cycle, and has become a major research focus ...

Use of Principal Components for Scaling Up Topographic Models to Map Soil Redistribution and Soil Organic Carbon

Landscape topography is a critical factor affecting soil formation and plays an important role in determining soil properties on the earth surface, as it regulates the gravity-driven soil movement induced by runoff and tillage activities. The recent application of Light Detection and Ranging (LiDAR) data holds promise for generating high spatial resolution topographic metrics that can be used to investigate soil property variability. In this study, fifteen topographic metrics derived from LiDAR data were used to investigate topographic impacts on redistribution of soil and spatial distribution of soil organic carbon (SOC). Specifically, we explored the use of topographic principal components (TPCs) for characterizing topography metrics and stepwise principal component regression (SPCR) to develop topography-based soil erosion and SOC models at site and watershed scales. Performance of SPCR models was evaluated against stepwise ordinary least square regression (SOLSR) models. Results showed that SPCR models outperformed SOLSR models in predicting soil redistribution rates and SOC density at different spatial scales. Use of TPCs removes potential collinearity between individual input variables, and dimensionality reduction by principal component analysis (PCA) diminishes the risk of overfitting the prediction models. This study proposes a new approach for modeling soil redistribution across various spatial scales. For one application, access to private lands is often limited, and the need to extrapolate findings from representative study sites to larger settings that include private lands can be important.

Landscape processes are critical components of soil formation and play important roles in determining soil properties and spatial structure in landscapes. We propose a new approach using stepwise principal component regression to predict soil redistribution and soil organic carbon across various spatial scales.

Landscape topography is a critical factor affecting soil formation and plays an important role in determining soil properties on the earth surface, as it ...