Name: spatial multiobjective optimization of agricultural conservation practices using a swat model and an evolutionary algorithm
Uploaded: 2012-12-09T17:00:00.000Z
Duration: 11 min 53 s
Channel: JoVE

K12 Standards

Pennsylvania State Academic Standards

9-12

Life Science

interdependent-relationships-in-ecosystems

Interdependent Relationships in Ecosystems

3.1.9-12.N

spatial-multiobjective-optimization-agricultural-conservation

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm

This research was funded in part from support received from the U.S. Environmental Protection Agency's Targeted Watersheds Grants Program (Project # WS97704801), the National Science Foundation's Dynamics of Coupled Natural and Human Systems (Project #DEB1010259-CARD-KLIN), and the U.S. Department of Agriculture-National Institute of Foodand Agriculture's Coordinated Agricultural Project (Project # 20116800230190-CARD-).

1. Prepare Watershed Model and Provide Input Data for Optimization
<ol>
	<li>Create an i_SWAT database.
	<ol>
		<li>Using a program called "rotator", build the database from multiple input databases including soils, weather, management and fertilizer.</li>
		<li>Alternatively, an existing SWAT run (possibly created with ArcSWAT or AVSWAT) can be imported with i_SWAT.exe. In this case, the program "swat_rewrite" can be used to replace management or other HRU information based on field-level data.</li>
		<li>Calibration and validation of the SWAT model should be performed at this point. The SWAT (version 2005) model incorporated within this Raccoon River Watershed EA modeling framework was originally calibrated and validated for a Total Maximum Daily Load (TMDL) study as described by Jha et al. (2010). Further calibration and validation of the SWAT model was conducted in support of the development of a Raccoon River Watershed Master Plan, as described in Agren, Inc. (2011), which is the SWAT model that was used for this study.</li>
		<li>Use a modified version of SWAT2005.exe, called SWAT2005GA.exe.</li>
	</ol>
	</li>
	<li>Prepare file "watershed presets.csv" - This is a text file storing many of the settings specific to the Raccoon watershed. It is read by GeneticiSWAT and MapSWAT below to set multiple controls and data fields for the watershed with one click.</li>
	<li>Prepare the costs of conservation practice elements. For this example, these are stored in table [Practice Costs - Raccoon by County] in a database "Practice costs by subbasin Josh.mdb".</li>
</ol>
The total cost of a candidate solution is the sum of costs of conservation practices applied to watershed units ("hydrologic response units", or HRUs). The optimization program considers an optimal assignment of a single conservation practice from a particular set of conservation practices in every cropland HRU in the watershed. The sets of possible conservation practices assigned to an HRU are called allele sets.
<ol start="4">
	<li>Create SWAT folders. For this run, 16 CPUs were used, meaning 16 copies of SWAT2005GA.exe were run in 16 separate folders (the same applies for systems with fewer CPUs, e.g. 4 folders should be created for a "quad-core" processor).</li>
</ol>
2. Select Optimization Parameters
<ol>
	<li>Optimization is controlled by the program called "GeneticISWAT". To perform optimization, open GeneticISWAT.exe.
	<ol>
		<li>Go to "File", then "Open" and select the i_SWAT database "Raccoon GA.mdb".</li>
		<li>Go to "File", then "Configuration" to assign the paths to SWAT model executables (SWAT2005GA.exe).</li>
		<li>Go to "Execute", then "Select Allele Set". This step determines the combinations of conservation practices used in optimization. For this run, allele set #14 was used, which has 23 combinations of conservation practices. Available allele sets are stored in the configuration file "Alleles.csv".</li>
		<li>Go to "Execute", then select "SPEA2 Archive Baseline Aware Subset" to perform multiobjective optimization using the SPEA2 evolutionary algorithm.</li>
	</ol>
	</li>
</ol>
<img alt="SWAT simulation setup interface showing parameters for watershed analysis and genetic algorithm settings." src="/files/ftp_upload/4009/4009fig1.jpg" data-altupdatedat="1787630408000" data-alt="Figure 1"> 
Figure 1. Setting optimization objectives and parameters.
Optimization parameters to be selected:
Preset: Select the watershed to be optimized. Clicking "Apply" selects entries from the presets file "watershed presets.csv" to fill control values on this screen.
Output Variable: Select the environmental objectives for optimization. As selected (N Outlet, P Outlet), this defines a 3-dimensional objective function: Nitrogen (Organic N + NO3 + NH4 + NO2) averaged for 5 years at the outlet, Phosphorus (Organic P + Mineral P) averaged for 5 years at the outlet, and the total cost of conservation practices. Note that this will create a 3-dimensional tradeoff frontier. Alternative output variables can be selected, where the multiobjective program is to minimize ({Output Variable}, Total Cost).
Population size: Set initial population size. This determines the initial number of candidate solutions. When "Seed with each allele" option is selected, candidate solutions representing a uniform application of each conservation practice specified in the allele set to all cropland HRUs in the watershed are created first. The remaining candidate solutions are created by a random assignment of conservation practices from the allele set to cropland HRUs. When selecting the "Seed with each allele" option, one needs to make sure that the initial population size is at least as large as the number of alleles in an allele set (23 in this demonstration).
Number of generations: Set the desired number of generations (iterations) for the optimization run (note that the run can be restarted).
Crossover probability: When two candidate solutions are selected for creating new candidate solutions, crossover probability specifies the probability that distinct new solutions are created (set to 1 for this demonstration).
Size of temporary population: This determines the number of new candidate solutions created. Processor resources are used most efficiently when this value is an integer multiple of the number of processor threads (16 in this demonstration).
Mutation probability: Specify the probability of random change in HRU assignment to another conservation practice from the allele set. (It is set to 0.03 for this demonstration).
Number of threads: Select the number of processors or threads used. 16 is used in this demonstration.
Curve No. calibration factor: This is provided from the SWAT model calibration.
Save Population in text file: This is important to select if one wishes to restart the optimization run after the specified number of iterations is completed. Checking this option produces a text file with the allele values of every HRU in every surviving candidate solution (individual). This can be read back in to restart and continue a run.
Secondary optimization parameters
First Year: Must be set to a year after start of historical weather information, and no later than 7 years before end of this data.
Price of Corn: Used with the yield loss equation to estimate the cost of fertilizer reductions.
Scoring Method: SPEA2 Archive. Scoring determines how likely a surviving individual is to be selected for crossover.
Purge Method: Dominated. Individuals which are worse in all 3 dimensions are dominated and purged.
HUC Source: Set to "Specified Location", meaning the value "7100006" from the following field "Watershed HUC" is used to find a row in the HUC Zone table. The value "07100006" is the eight-digit HUC code for the Raccoon watershed.
Cost Source: Set to "County (HRU Location Code)" to indicate that costs other than CRP will be determined by county FIPS codes in the practice costs table above.
Cost Source CRP: Set to "1 Location" to indicate that CRP cost will be determined by county FIPS codes in the practice costs table above.
SWAT version: SWAT2005
3. Representative Results
GeneticiSWAT.exe produces a log file showing the settings and results for all candidate solutions (individuals), as well as a "save" file which encodes the results from the final algorithm iteration and which can be used to restart the optimization run.
At this point, one can visualize the entire set of Pareto-efficient solutions (the tradeoff frontier) by following the steps below:
<ol>
	<li>Run GeneticiSWAT;
	<ol>
		<li>Go to "File", then "Open" to open the i_SWAT database "Raccoon GA.mdb".</li>
		<li>Go to "Execute", then "Export HRU List". Save file as "Raccoon Allele HRU.txt".</li>
	</ol>
	</li>
	<li>Produce an animation by running Mapswat.exe, selecting "Execute" and then "3d Animation".</li>
</ol>
<img alt="Run Data 3D software interface; simulation setup with log files, parameters for 3D watershed analysis." src="/files/ftp_upload/4009/4009fig2.jpg" data-altupdatedat="1787630408000" data-alt="Figure 2"> 
Figure 2. Screenshot for creating "snapshots" for 3-dimensional frontier visualization.
Output is a series of files which can be rendered all at once into image files by using POV-RAY program and selecting "Render", then "File Queue". The images can be used on their own or combined into a movie showing the algorithm progression.
<img alt="3D genetic drift simulation graph, showcasing evolutionary progression over generations." src="/files/ftp_upload/4009/4009fig3.jpg" data-altupdatedat="1787630408000" data-alt="Figure 3"> 
Figure 3. Static visualization of the tradeoff frontier.
If desired, a movie showing the algorithm progression can be created by running "Framescanner.exe" and following these steps:
<ol>
	<li>Go to "File", then "New", then "File", then "Import", then "PNG Files". Select the static images.</li>
	<li>To create a movie, go to "File", then "Export", then "AVI".</li>
	<li>Select codec "DIB" to create AVI files from batches of image files.</li>
</ol>
Each point in the frontier represents a watershed configuration (a specific assignment of conservation practices on a landscape). Maps of these configurations can be seen for the entire frontier by following these steps:
<ol>
	<li>Run Mapswat.exe, select "Execute", then "Map Animation".</li>
	<li>Select "Raccoon" from preset list and click "Apply".</li>
	<li>Select "Layout 7 (Raccoon)" from Map Layout list, then click "OK".</li>
</ol>
<img alt="Hydrological modeling interface, SWAT setup, parameters, watershed data, pollutant input, subbasins." src="/files/ftp_upload/4009/4009fig4.jpg" data-altupdatedat="1787630408000" data-alt="Figure 4"> 
Figure 4. Screenshot of creating a map of each individual in the final frontier.
Exporting specific watershed configurations (individuals) of interest. 
Often a question of interest is to select specific watershed configurations (individuals) achieving particular water quality objectives. For example, one may wish to find an individual in the frontier which reduces Nitrogen by 30% and Phosphorus by 20% relative to baseline loadings. MapSWAT allows one to search the frontier for the individual with the smallest Euclidean distance to the specified objective. This can be done by doing the following:
<ol>
	<li>Open MapSWAT.exe. Select "Execute" | "Search".</li>
</ol>
<img alt="Software interface for managing log files and setting optimization parameters in data analysis." src="/files/ftp_upload/4009/4009fig5.jpg" data-altupdatedat="1787630408000" data-alt="Figure 5"> 
Figure 5. Screenshot of searching for a specific individual in the frontier based on water quality objectives.
<ol start="2">
	<li>Enter minimum and maximum reduction targets Tmin and Tmax as well as an interval Tint. Also enter a specific percent reduction in Nitrogen (Nspec) from baseline in the "% reduction" space next to N Baseline, and percent reduction in Phosphorus (Pspec) in the "% reduction" next to Phosphorus baseline. The program produces output in a popup screen:</li>
</ol>
<img alt="Static equilibrium equations, data table results; calculations and numerical analysis crucial for research." src="/files/ftp_upload/4009/4009fig6.jpg" data-altupdatedat="1787630408000" data-alt="Figure 6"> 
Figure 6. Screenshot of search output
<ol start="3">
	<li>Click "Copy Text" and paste into a spreadsheet. Three tables are produced. In the first are individuals nearest to N and P targets of the same percent reduction, which ranges from Tmin to Tmax by Tint. Just below this the closest single individual to the target (Nspec, Pspec) appears. Second, a table giving nearest individuals where the P target ranges from Tmin to Tmax while N is held constant near Nspec. Third, a table giving individuals nearest N targets ranging from Tmin to Tmax while P is held constant near Pspec. In this case, the closest individual to a 30% N reduction was ID 8423 with an N value of 14,637,279.60. Here is the map showing the spatial distribution of conservation practices and the location of this watershed configuration in the tradeoff frontier:</li>
</ol>
<img alt="Cost and phosphorus reduction chart with geographic map; agricultural impact analysis." src="/files/ftp_upload/4009/4009fig7.jpg" data-altupdatedat="1787630408000" data-alt="Figure 7"> 
Figure 7. Screenshot of a sample map describing the selected individual in the frontier. <a href="https://www.jove.com/files/ftp_upload/4009/4009fig7large.jpg" target="_blank"> Click here to view larger figure</a>.
Exporting map data for further analysis is possible by following these steps:
<ol>
	<li>Run Mapswat.exe, select "Execute", then "Export Map Data".</li>
	<li>Select "Raccoon" from preset list and click "Apply".</li>
	<li>Enter the ID of a watershed configuration (individual) (8423 shown), check "Show Allele Properties" and "Show Costs", and then click "OK". This data can be used to create custom maps of the selected watershed configuration using a GIS program.</li>
</ol>
<table border="1">
	<tbody>
		<tr>
			<td>Name of Program</td>
			<td>Source</td>
			<td>Description</td>
		</tr>
		<tr>
			<td>Rotator</td>
			<td>CARD</td>
			<td>Creates and fills an i_SWAT database with soil, weather, and management data for a watershed.</td>
		</tr>
		<tr>
			<td>Swat2005GA.exe</td>
			<td>USDA Grassland, Soil &amp; Water Research Laboratory</td>
			<td>Watershed simulation model</td>
		</tr>
		<tr>
			<td>i_SWAT.exe</td>
			<td>CARD</td>
			<td>SWAT database interface</td>
		</tr>
		<tr>
			<td>GeneticISWAT.exe</td>
			<td>CARD</td>
			<td>Evolutionary algorithm SWAT controller. Incorporates GALib from <a href="http://lancet.mit.edu/ga/" target="_blank">http://lancet.mit.edu/ga/</a>.</td>
		</tr>
		<tr>
			<td>MapSWAT.exe</td>
			<td>CARD</td>
			<td>Reads i_SWAT databases and shapefiles, produces images of generations and individuals.</td>
		</tr>
		<tr>
			<td>POV-Ray</td>
			<td>Povray.org</td>
			<td>Persistence of Vision raytracer.</td>
		</tr>
		<tr>
			<td>Framescanner.exe</td>
			<td>Todd Campbell</td>
			<td>PNG image to AVI converter</td>
		</tr>
		<tr>
			<td>Windows Live Movie Maker</td>
			<td>Microsoft</td>
			<td>Used to compress AVI to WMV</td>
		</tr>
	</tbody>
</table>
Table 1. Table of programs required.
<table border="1">
	<tbody>
		<tr>
			<td>Name of File</td>
			<td>Type</td>
			<td>Description</td>
		</tr>
		<tr>
			<td>Raccoon GA.mdb</td>
			<td>Access database</td>
			<td>Structure and management descriptions of Raccoon watershed. Read by GeneticiSWAT and MapSWAT.</td>
		</tr>
		<tr>
			<td>watershed presets.csv</td>
			<td>Text</td>
			<td>Setting presets for GeneticiSWAT.exe and MapSWAT</td>
		</tr>
		<tr>
			<td>Alleles.csv</td>
			<td>Text</td>
			<td>List of allele sets for evolutionary algorithm.</td>
		</tr>
		<tr>
			<td>Raccoon Allele HRU.txt</td>
			<td>Text</td>
			<td>File created by GeneticISWAT listing those alleles determined to be cropland. Read by MapSWAT.</td>
		</tr>
		<tr>
			<td>Practice costs by subbasin Josh.mdb</td>
			<td>Access Database</td>
			<td>Costs by management practice and county.</td>
		</tr>
		<tr>
			<td>Terrace Zones.mdb</td>
			<td>Access Database</td>
			<td>Table [HUC Data] holds the terrace and yield zone numbers for the watershed.</td>
		</tr>
		<tr>
			<td>NRI Budgets.mdb</td>
			<td>Access Database</td>
			<td>Read by GeneticISWAT.exe for crop &amp; machine tables which are not used in this run.</td>
		</tr>
		<tr>
			<td>phucrp 2008-12-15.dat</td>
			<td>Text</td>
			<td>Plant Heat Unit lookup table, not used in this run.</td>
		</tr>
		<tr>
			<td>Management.mdb</td>
			<td>Access Database</td>
			<td>Rotation lookup table, not used in this run.</td>
		</tr>
		<tr>
			<td>Raccoon GA 2011-09-28 1313.log, Raccoon GA 2011-09-29 0732.log, Raccoon GA 2011-10-07 0644.log</td>
			<td>Text</td>
			<td>Log files of GeneticISWAT run.</td>
		</tr>
		<tr>
			<td><a href="https://www.jove.com/files/ftp_upload/4009/Raccoon_GA.wmv">Raccoon GA.wmv</a></td>
			<td>Animation</td>
			<td>3d display of individuals by generation</td>
		</tr>
		<tr>
			<td><a href="https://www.jove.com/4009/Subbasin.shp" target="_blank">Subbasin.shp</a></td>
			<td>ESRI Shapefile</td>
			<td>Outlines of subbasins in the watershed.</td>
		</tr>
		<tr>
			<td><a href="https://www.jove.com/files/ftp_upload/4009/Raccoon_Map.wmv" target="_blank">Raccoon Map.wmv</a></td>
			<td>Animation</td>
			<td>Display of dominant alleles for each subbasin for each individual on the frontier.</td>
		</tr>
	</tbody>
</table>
Table 2. Table of sample files required.

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<li>Rabotyagov, S., Jha, M., Campbell, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Impact+of+crop+rotations+on+optimal+selection+of+conservation+practices+for+water+quality+protection%5BTitle%5D)+AND+%22J.+Soil.+Water+Conserv%22%5BJournal%5D)">Impact of crop rotations on optimal selection of conservation practices for water quality protection.</a> J. Soil. Water Conserv. 65 (6), 369-380 (2010).</li>
<li>Rabotyagov, S. S., Jha, M., Campbell, T. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Nonpoint-source+pollution+for+an+Iowa+watershed%3A+An+application+of+evolutionary+algorithms%5BTitle%5D)+AND+%22Canadian+Journal+of+Agricultural+Economics%2FRevue+canadienne+d%27agroeconomie%22%5BJournal%5D)">Nonpoint-source pollution for an Iowa watershed: An application of evolutionary algorithms.</a> Canadian Journal of Agricultural Economics/Revue canadienne d'agroeconomie. , (2010).</li>
<li>Rabotyagov, S. S., Jha, M., Campbell, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Searching+for+Efficiency%3A+Least+Cost+Nonpoint+Source+Pollution+Control+with+Multiple+Pollutants%2C+Practices%2C+and+Targets%5BTitle%5D)+AND+%22J.+Nat.+and+Environ.+Sci%22%5BJournal%5D)">Searching for Efficiency: Least Cost Nonpoint Source Pollution Control with Multiple Pollutants, Practices, and Targets.</a> J. Nat. and Environ. Sci. 1, 75-90 (2010).</li>
<li>Ribaudo, M. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Consideration+of+off-site+impacts+in+targeting+soil+conservation+programs%5BTitle%5D)+AND+%22Land+Econ%22%5BJournal%5D)">Consideration of off-site impacts in targeting soil conservation programs.</a> Land Econ. 62, 402-411 (1986).</li>
<li>Ribaudo, M. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Targeting+the+conservation+reserve+program+to+maximize+water+quality+benefits%5BTitle%5D)+AND+%22Land+Econ%22%5BJournal%5D)">Targeting the conservation reserve program to maximize water quality benefits.</a> Land Econ. 65, 320-332 (1989).</li>
<li>Srivastava, P., Hamlett, J. M., Robillard, P. D., Day, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Watershed+optimization+of+best+management+practices+using+AnnAGNPS+and+a+genetic+algorithm%5BTitle%5D)+AND+%22Water+Resour.+Res%22%5BJournal%5D)">Watershed optimization of best management practices using AnnAGNPS and a genetic algorithm.</a> Water Resour. Res. 38 (3), 1-14 (2002).</li>
<li>Veith, T. L., Wolfe, M. L., Heatwole, C. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Development+of+optimization+procedure+for+cost-effective+BMP+placement%5BTitle%5D)+AND+%22J.+Am.+Water+Resour.+Assoc%22%5BJournal%5D)">Development of optimization procedure for cost-effective BMP placement.</a> J. Am. Water Resour. Assoc. 39 (6), 1331-1343 (2003).</li>
<li>GAlib: Matthew's Genetic Algorithms Library [Internet]. , Available from: 
 <a target="_blank" href="http://lancet.mit.edu/ga/">http://lancet.mit.edu/ga/</a> (1996).</li>
<li>Whittaker, G., Confesor, R., Griffith, S. M., Färe, R., Grosskopf, S., Steiner, J. J., Mueller-Warrant, G. W., Banowetz, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+Hybrid+Genetic+Algorithm+for+Multiobjective+Problems+with+Activity+Analysis-based+Local+Search%5BTitle%5D)+AND+%22Eur.+J.+Operat.+Res%22%5BJournal%5D)">A Hybrid Genetic Algorithm for Multiobjective Problems with Activity Analysis-based Local Search.</a> Eur. J. Operat. Res. , (2007).</li>
<li>Zitzler, E., Laumanns, M., Thiele, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((SPEA2%3A+Improving+the+Strength+Pareto+Evolutionary+Algorithm+for+Multiobjective+Optimization%5BTitle%5D)+AND+%22CIMNE%22%5BJournal%5D)">SPEA2: Improving the Strength Pareto Evolutionary Algorithm for Multiobjective Optimization.</a> CIMNE. , 95-100 (2002).</li>
</ol>

No conflicts of interest declared.

We build an integrated simulation-optimization framework to search for Pareto-efficient sets of watershed configurations involving lowest-cost mix and location of agricultural conservation practices to achieve a range of watershed-level nutrient reduction objectives. A conceptual diagram of the simulation-optimization system is presented in Figure 8. Watershed simulation, including simulating the water quality impacts of agricultural conservation practices are handled by the hydrologic model, SWAT2005, c...

spatial multiobjective optimization of agricultural conservation practices using a swat model and an evolutionary algorithm

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,5,12,20) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization.
Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods3,4,9,10,13-15,17-19,22,23,25. In this application, we demonstrate a program which follows Rabotyagov et al.'s approach and integrates a modern and commonly used SWAT water quality model7 with a multiobjective evolutionary algorithm SPEA226, and user-specified set of conservation practices and their costs to search for the complete tradeoff frontiers between costs of conservation practices and user-specified water quality objectives. The frontiers quantify the tradeoffs faced by the watershed managers by presenting the full range of costs associated with various water quality improvement goals. The program allows for a selection of watershed configurations achieving specified water quality improvement goals and a production of maps of optimized placement of conservation practices.

This work demonstrates an integration of a water quality model with an optimization component utilizing evolutionary algorithms to solve for optimal (lowest-cost) placement of agricultural conservation practices for a specified set of water quality improvement objectives. The solutions are generated using a multi-objective approach, allowing for explicit quantification of tradeoffs.

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals ...

The overall goal of the following experiment is to demonstrate the method for multi objective optimization of conservation practices in a watershed using a simulation optimization system involving the watershed process model, and an evolutionary algorithm. The overarching question is how to allocate agricultural conservation practices in a watershed. So water quality objectives are met at the lowest cost.Multiple conservation practices are possible on each field, and multiple water quality objectives may be important. A particular assignment of conservation practices can be simulated by a watershed process model. To achieve the optimization goal first, select a calibrated and validated watershed process model and model representations of conservation practices.As a second step, the environmental objectives to be maximized are selected and costs of conservation practices are obtained, which allow for the evolutionary algorithm component looking to simultaneously optimize along environmental and cost objectives to be invoked. Next, selection of parameters controlling optimization is done in order to perform multi objective optimization. These two components, simulation and optimizati

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passaging hues human embryonic stem cell-lines with trypsin.

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Passaging HuES Human Embryonic Stem Cell-lines with Trypsin.

In this video we demonstrate how our lab routinely passages HuES human embryonic stem cell lines with trypsin. Brought to you by JoVE.

freezing human es cells

Freezing Human ES Cells

Here we demonstrate how our lab freezes HuES human embryonic stem cell lines.

dissection of drosophila ovaries

Dissection of Drosophila Ovaries

assay for adhesion and agar invasion in s. cerevisiae

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Assay for Adhesion and Agar Invasion in S. cerevisiae

We describe a qualitative assay for yeast adhesion and agar invasion as a measure of invasive and pseudohyphal differentiation. This simple assay can be used to assess the invasive phenotype of various mutants as well as the effects environmental cues and signaling pathways on yeast differentiation.

monitoring actin disassembly with time-lapse microscopy

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Monitoring Actin Disassembly with Time-lapse Microscopy

a rapid technique for the visualization of live immobilized yeast cells

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A Rapid Technique for the Visualization of Live Immobilized Yeast Cells

A rapid technique for the visualization of growing immobilized yeast cells, here applied to fluorescent reporters at the silent mating loci HML and...

dissection of larval cns in drosophila melanogaster

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Dissection of Larval CNS in Drosophila Melanogaster

In this article we demonstrate how to dissect the central nervous system from third instar Drosophila larvae.

human es cells: starting culture from frozen cells

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Human ES cells: Starting Culture from Frozen Cells

Here we demonstrate how our lab begins a HuES human embryonic stem cell line culture from a frozen stock.

light/dark transition test for mice

Light/dark Transition Test for Mice

The light/dark transition test is one of the most widely used tests to measure anxiety-like behavior in mice. Here, we present a movie that shows detailed procedures on how we conduct the test.

horizontal slice preparation of the retina

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Horizontal Slice Preparation of the Retina

Traditionally the vertical slice and the whole-mount preparation of the retina have been used to study the function of retinal circuits. Here, we describe the novel slicing method to preserve the dendritic morphology of retinal neurons intact.

gibberella zeae ascospore production and collection for microarray experiments.

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Gibberella zeae Ascospore Production and Collection for Microarray Experiments.

To study the developmental processes of ascospores in Gibberella zeae, a procedure for collection under sterile conditions is filmed in order to generate the highest level of information for protocol description. This should facilitate the reproducibility of the experiment, a crucial aspect when full genome expression profile tests are implemented.

nuclear transfer into mouse oocytes

Nuclear Transfer into Mouse Oocytes

This movie and the protocol are intended to help learning nuclear transfer.

measuring exocytosis in neurons using fm labeling

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Measuring Exocytosis in Neurons Using FM Labeling

The ability to measure the kinetics of vesicle release can help provide insight into some of the basics of neurotransmission. Here we used real-time imaging of vesicles labeled with the red fluorescent dye FM 4-64 to measure the rate of presynaptic vesicle release in hippocampal neuronal cultures.

es cell-derived neuroepithelial cell cultures

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ES Cell-derived Neuroepithelial Cell Cultures

Derivation of neuroepithelial precursors from embryonic stem (ES) cells using stromal cell-derived inducing activity (SDIA).

propagation of human embryonic stem (es) cells

propagation-of-human-embryonic-stem-es-cells

Propagation of Human Embryonic Stem (ES) Cells

long-term imaging mammalian cells using wide-field microscopy

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Long-term Imaging Mammalian Cells using Wide-Field Microscopy

gene-gun transfection of hippocampal neurons

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Gene-gun Transfection of Hippocampal Neurons

testing visual sensitivity to the speed and direction of motion in lizards

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Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in lizards using an operant conditioning paradigm that employs video playback of random-dot kinematograms and computer-generated invertebrates.

mouse adrenal chromaffin cell isolation

Mouse Adrenal Chromaffin Cell Isolation

Adrenal medullary chromaffin cell culture systems are extremely useful for the study of excitation-secretion coupling in an in vitro setting.  This protocol illustrates the method used to dissect the adrenals and then isolate the medullary region by stripping away the adrenal cortex.  The digestion of the medulla into single chromaffin cells is then demonstrated.

growth factor-coated bead placement on dorsal forebrain explants

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Growth Factor-Coated Bead Placement on Dorsal Forebrain Explants

This video demonstrates two methods for preparing and placing beads, which have been coated with growth factor, on explants of the developing cerebral cortex.   These beads can be used to induce spatially restricted gene expression on developing neural tissue such as forebrain explants.  Methods are given for using both Affi-Gel beads and heparin acryllic beads.

mouse dorsal forebrain explant isolation

Mouse Dorsal Forebrain Explant Isolation

This video demonstrates the protocol for isolating and culturing explants of the mouse forebrain from embyonic day 12 mice.  Procedures for removal of the uterus, embryos from uterus, and dissection of embryos are given.  In addition the methodology for transferring these explants onto specialized membranes on which they are cultured is demonstrated.  The development of the forebrain can be studied in vitro using this preparations as well as changes in gene expression.

dissection of imaginal discs from 3rd instar drosophila larvae

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Dissection of Imaginal Discs from 3rd Instar Drosophila Larvae

This protocol demonstrates the dissection technique used for isolating imaginal discs from drosophila larvae at the 3rd instar stage.  Methods for fixing the tissue after saying and removing the wing, leg, and eye discs are demonstrated directly on a microscope slide for subsequent visualization.

culture of mouse neural stem cell precursors

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Culture of Mouse Neural Stem Cell Precursors

This video describes the method used for isolation of neuroprecursors from the developing cortex of embryonic mice.  The procedure for removing embryos from the uterus, dissecting the cortical tissue, and digesting the isolated cerebral cortex is shown.

studying aggression in drosophila (fruit flies)

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Studying Aggression in Drosophila (fruit flies)

Aggression is an innate behavior that evolved in the framework of defending or obtaining resources.  This complex social behavior is influenced by ...

interview with edward kravitz

Interview with Edward Kravitz

isolation and transplantation of hematopoietic stem cells (hscs)

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Isolation and Transplantation of Hematopoietic Stem Cells (HSCs)

wolbachia bacterial infection in drosophila

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Wolbachia Bacterial Infection in Drosophila

transplantation of whole kidney marrow in adult zebrafish

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Transplantation of Whole Kidney Marrow in Adult Zebrafish

In this article, we demonstrate a method to perform HCT in adult zebrafish.

dissection of 6.5 dpc mouse embryos

Dissection of 6.5 dpc Mouse Embryos

Isolation of postimplantation-stage embryos allows one to study gene patterning and analyze cell-lineage decision making processes during embryonic development, but proper dissection of the early embryo can be challenging. This protocol describes a method for isolating early primitive-streak-stage embryos (~6.5 days post coitum [dpc]).

derivation of hematopoietic stem cells from murine embryonic stem cells

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Derivation of Hematopoietic Stem Cells from Murine Embryonic Stem Cells

This protocol details the derivation of transplantable hematopoietic stem cells from mouse embryonic stem cells (ESC) and their subsequent injection into lethally irradiated recipient mice.  Briefly, ESC are differentiated as embryoid bodies, which are then infected with retroviral HoxB4 and co-cultured with OP9 stromal cells and hematopoietic cytokines.

tracheotomy: a method for transplantation of stem cells to the lung

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Tracheotomy: A Method for Transplantation of Stem Cells to the Lung

Significant breakthroughs in stem cell identification are continuously being made. To translate these discoveries, however, novel methods for cellular delivery must be devised. Here I report that the airways provide a safe route for stem cell transplantation to the lungs.

denaturing gradient gel electrophoresis (dgge)

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Denaturing Gradient Gel Electrophoresis (DGGE)

christopher hughes:  an in vitro model for the study of angiogenesis (interview)

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Christopher Hughes:  An in vitro model for the Study of Angiogenesis (Interview)

Christopher C.W. Hughes describes the utility of his culture system for studying angiogenesis in vitro.  He explains the importance of fibroblasts that secrete a critical, yet unidentified, soluble factor that allow endothelial cells to form vessels in culture that branch, form proper lumens, and undergo anastamosis.

isolation of human umbilical vein endothelial cells (huvec)

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Isolation of Human Umbilical Vein Endothelial Cells (HUVEC)

This video protocol illustrates the isolation and culture of human umbilical vein endothelial cells (HUVEC) from human umbilical cord. Once isolated these cells can be used for in vitro angiogenesis assays like the Optimized Fibrin Gel Bead Assay also demonstrated by the Hughes lab.<br...

harvesting sperm and artificial insemination of mice

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Harvesting Sperm and Artificial Insemination of Mice

This protocol demonstrates methods for extracting sperm from the testes of males and then inseminating female mice.   This procedure is useful when precise time is needed in developmental studies as well as transgenic work.

retrieval of mouse oocytes

Retrieval of Mouse Oocytes

This protocol illustrates the technique for extracting oocytes or early-stage fertilized embryos from the oviduct of mice. The ability to identify the infindibulum and insert a blunt end needle into it is essential to correctly performing the procedure.

optimized fibrin gel bead assay for the study of angiogenesis

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Optimized Fibrin Gel Bead Assay for the Study of Angiogenesis

This video demonstrates the protocol of an in vitro angiogenesis assay that recapitulates several stages of angiogenesis.  Time-lapse images of sprouting, lumen formation, branching and anastomosis - key features of angiogenesis - are shown.

dissection of organizer and animal pole explants from xenopus laevis embryos and assembly of a cell adhesion assay

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Dissection of Organizer and Animal Pole Explants from Xenopus laevis Embryos and Assembly of a Cell Adhesion Assay

This video demonstrates the technique used for preparation of organizer and animal pole explants from Xenopus laevis embryos, including the use of the eyebrow knife - a specialized dissection tool made of one's eyebrow.  The protocol for assembling an adhesion assay is also given, which probes for the presence of key adhesion molecules present on the surface organizer or animal pole cells that are critical for proper development.

plastic embedding and sectioning of xenopus laevis embryos

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Plastic Embedding and Sectioning of Xenopus laevis Embryos

Plastic sections maintain true tissue morphology in thin sections of tissue that can be immunostained with fluorescent secondary antibodies, making this method more useful than paraffin-embedded or frozen sections for many types of tissue.  The method for staining, plastic embedding, and sectioning is demonstrated in this video.

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Ole Isacson: Development of New Therapies for Parkinson's Disease

Ole Isacson gives a concise overview of Parkinsons's disease, its causes, therapeutic strategies, and advances in Parkinson's research.

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Organotypic Culture of Adult Rabbit Retina

This article demonstrates the dissection and incubation of rabbit retina and particle-mediated gene transfer of plasmids encoding GFP or a variety of subcellular markers into retinal ganglion cells.

maldi sample preparation: the ultra thin layer method

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MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

proboscis extension response (per) assay in drosophila

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Proboscis Extension Response (PER) Assay in Drosophila

Proboscis extension response or PER is a taste behavior assay that has been used in flies as well as in honeybees.  When the proboscis makes contact with an attractive substance, the fly extends its proboscis to consume the substance. Solutions of various sugars are very attractive to the fly.

thin sectioning of slice preparations for immunohistochemistry

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Thin Sectioning of Slice Preparations for Immunohistochemistry

The present method allows reproducible cryostat sectioning of small, difficult-to-manage, tissue pieces, such as biopsies and brain slices.  We utilize a simple aluminum freezing stage to facilitate handling of tissue and a standard cryostat to routinely produce 5-10 micron serial sections from 400 micron thick brain slices.

extracting dna from the gut microbes of the termite (zootermopsis angusticollis) and visualizing gut microbes

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Extracting DNA from the Gut Microbes of the Termite (Zootermopsis Angusticollis) and Visualizing Gut Microbes

This video illustrates the technique for extracting DNA from the species of microbes resident in the termite hindgut.  The preparation of a wet mount slide, which is useful for visualizing the gut microbial community is also illustrated, and a tour through the species-rich gut environment is given.

investigating the microbial community in the termite hindgut - interview

investigating-the-microbial-community-in-the-termite-hindgut-interview

Investigating the Microbial Community in the Termite Hindgut - Interview

Jared Leadbetter explains why the termite-gut microbial community is an excellent system for studying the complex interactions between microbes.     The symbiotic relationship existing between the host insect and lignocellulose-degrading gut microbes is explained, as well as the industrial uses of these microbes for degrading plant biomass and generating biofuels.

layers of symbiosis - visualizing the termite hindgut microbial community

layers-symbiosis-visualizing-termite-hindgut-microbial

Layers of Symbiosis - Visualizing the Termite Hindgut Microbial Community

Jared Leadbetter takes us for a nature walk through the diversity of life resident in the termite hindgut - a microenvironment containing 250 different species found nowhere else on Earth.  Jared reveals that the symbiosis exhibited by this system is multi-layered and involves not only a relationship between the termite and its gut inhabitants, but also involves a complex web of symbiosis among the gut microbes themselves.

flash freezing and cryosectioning e12.5 mouse brain

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Flash Freezing and Cryosectioning E12.5 Mouse Brain

Demonstrated in this video are the techniques for flash freezing and sectioning embryonic brain tissue from mouse.  Useful tips for using the cryostat are given, including troubleshooting methods that can be used while cutting to ensure that the resultant tissues sections are free of cracks and other distortions.

primary neuronal cultures from the brains of late stage drosophila pupae

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Primary Neuronal Cultures from the Brains of Late Stage Drosophila Pupae

This video demonstrates the preparation of primary neuronal cultures from the brains of late stage Drosophila pupae. Views of live cultures show neurite outgrowth and imaging of calcium levels using Fura-2.

large-scale screens of metagenomic libraries

large-scale-screens-of-metagenomic-libraries

Large-Scale Screens of Metagenomic Libraries

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation.  Generating a ...

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