The authors acknowledge the financial support of NSFC to WT (grant no. 41272368) and QKX (grant no. 41630205).

NOTE: The data processing procedures include: synthetic seismogram calculation, synthetic-real seismic trace correlation, and geo-body extraction. Below are the step-by-step details of each procedure.
1. Calculation of Synthetic Seismogram
<ol>
	<li>Calculate the acoustic impedance at each interval of the down-well logging curve. 
	NOTE: Acoustic impedance is the product of &#39;seismic wave velocities&#39; and &#39;density&#39; (&#961;*&#957;)). The data are often averaged to sampling intervals larger than 1 ft, in order to reduce the computation time and aliasing.</li>
	<li>Calculate the reflection coefficients (R0) at each interface by using the acoustic impedance calculation: 
	<img alt="Equation" src="/files/ftp_upload/55930/55930eq1.jpg" /> 
	where &#957;1 and &#957;2 are the averaged velocities of the layers below and above the interface, respectively; &#961;1 and &#961;2 are the corresponding averaged densities.
	<ol>
		<li>If the well does not intersect the igneous bodies, use nearby wells that have intersected the target rocks to obtain the parameters (velocity, density, etc.).</li>
	</ol>
	</li>
	<li>Chose a wavelet that has an amplitude and phase spectrum similar to that of the nearby seismic data.</li>
	<li>Convolve the synthetic wavelet with the reflection series for the entire well survey and generate a synthetic seismic trace. The final simulated seismic trace T(t) can be described by the convolutional model as below: 
	<img alt="Equation" src="/files/ftp_upload/55930/55930eq2.jpg" /> 
	where R0(t) is the reflection coefficient, w(t) is the wavelet and n(t) is the noise.</li>
	<li>If the frequency of the seismic data has large variations throughout the whole well, re-compute the synthetic seismic trace using a wavelet with a different phase and a dominant frequency at different depth intervals.
	<ol>
		<li>Repeat the process if the match between the synthetic trace and the seismic data is not satisfactory.</li>
	</ol>
	</li>
	<li>Perform the calculation with the provided software (e.g., Petrel E&#38;P Software Platform).
	<ol>
		<li>Start the software. Select File | Open Project | and then select the demo research project tlm (users can select their own desired projects). The project should contain well data, wired log, well tops, seismic cube, and interpretation surface in the research area.</li>
		<li>Click on Home | Windows | 2D Windows | 3D Windows to open two display windows to show the data sets according to user&#39;s preference.</li>
		<li>In the &#34;Wells Tree of Input Pane&#34;, right click the desired well. Open the Settings window of the well and select the Time tab to create a new time log. Select Velocity Function, then select DT data in the new time log. Click the OK button to close settings window. A new one-way time log is automatically created and will be shown in the &#34;Wells Tree of Input Pane&#34;. 
		NOTE: A one-way time log is a time-depth relationship of this well. Wired log domains can be transformed to time domains and be shown in the time domain window.</li>
		<li>Activate an existing 3D Window by clicking the displayed window. If there is no 3D Window displayed, create a new 3D Window by clicking Home | Windows | 3D Windows. Select TWT in the toolbar of the 3D Window to show the 3D Window in time domain.</li>
		<li>Select representative wired logs (such as &#39;GR&#39;, &#39;DT&#39;, or &#39;RT&#39;) in the Wells Tree to show them in the 3D Window; at the same time, select the seismic profile in the &#39;seismic&#39; tree of the &#39;input&#39; pane to show them in the same 3D Window.</li>
		<li>Use the Manipulate Plane tool in the toolbar of the 3D Window to adjust the location of the profile to intersect the well; the user will see that the wired log has been transformed to the time domain and displayed with the seismic profile in the same 3D window.</li>
		<li>Click Seismic Interpretation | Seismic Well Tie | Seismic Well Tie Process. Choose Integrated Seismic Well Tie in the type of study row, and add desired well in the Well row. Choose calibrated one-way time log as time-depth relationship in the TDR row of the input tab, choose seismic cube in the seismic row. Choose any log in the RC calculation method.</li>
		<li>Click Launch Wavelet Toolbox to create a Ricker wavelet to apply in this process. Click OK and a new well section window and synthetic seismogram display will be created.</li>
	</ol>
	</li>
</ol>
2. Correlate the Synthetic Traces with the Real Seismic Reflectors
<ol>
	<li>Use an automated correlation application, like Seismic Well Tie in the platform, to adapt the resulting synthetic trace to the vertical scale of the seismic section.</li>
	<li>Adjust the synthetic seismogram to increase the overlapping of high amplitude reflectors of the synthetic trace and real trace.</li>
	<li>Adjust the synthetic seismogram and the real trace repeatedly. When the overlapping trace reaches the maximum, the interpreter has reached the &#34;best fits&#34; between the obtained synthetic seismogram and real traces.
	<ol>
		<li>Repeat the process until the correlations reach the desired level.</li>
	</ol>
	</li>
	<li>Perform the correlation with the provided software.
	<ol>
		<li>Activate the window created in step 1.6.3, which is the one-way time log automatically created from the acoustic log. 
		NOTE: This automatically created &#39;one-way time log&#39; is not perfectly correlated with the real seismic reflectors. The users should calibrate the correlations between the one-way time log and the real seismic reflectors.</li>
		<li>To calibrate their correlations, choose a continual and representative reflector that is intersected by the well. Then manually adjust the depth of the well log. For example, to adjust the depth of the DT log, right click the One-Way Time Log in well tree | select the Calculator tool | then add a small time increment (for example, 10 ms) by typing &#39;DT=DT+10&#39; in the input dialog of the Calculator tool.</li>
		<li>If the &#39;10 ms&#39; increment is too large or too small, change the increment to another time (can be negative value) in the &#39;calculator&#39; tool. Check the correlation between the well log and the selected seismic horizon repeatedly and then adjust the time increment repeatedly, until the correlation is perfectly calibrated.</li>
	</ol>
	</li>
</ol>
3. Extraction of Basaltic Sills
<ol>
	<li>Pick 2 high-amplitude reflectors encasing the target sills. 
	NOTE: Most intrusions are expressed in seismic data as tuned reflection packages, whereby the reflections from the upper and lower intrusion contacts cannot be distinguished. Tuning occurs when the vertical intrusion thickness is between &#955;/4 and &#955;/8 (&#955; is seismic wavelength)19. Therefore, sills are shown as a set of strong reflections in the seismic section, and their apparent thickness is false.</li>
	<li>Extract probes between the horizons corresponding to the two high-amplitude reflectors. 
	NOTE: There are different tools based on the rendering technique that can help the interpreters better visualize the targets, such as &#34;box probes&#34;, &#34;surfaces probes&#34; and &#34;well probes&#34;. However, for identification of contacts between the sills and encasing strata, the best tool is &#34;surface probe&#34;. (&#34;Surface probe, etc.&#34; are terms in &#39;Petrel&#39; software. The software users should be familiar with these terms).</li>
	<li>Remove the areas surrounding the geological objects of interest by changing the Voxel connectivity opacity threshold value. Set the default threshold value to 20%. The visualization method of &#34;opacity rendering&#34; is used here to display the result of the extraction of basaltic sills ( Figure 2C). 
	NOTE: There are high amplitude reflections along the surface between igneous rock and sedimentary rock because of their significant difference in acoustic impedance. Make the low amplitude parts transparent to highlight the shape of the igneous bodies.</li>
	<li>As the value for isolation can be higher than 20 - 30%, change the value with small increments to make sure all important igneous bodies are not lost; the larger the value, the higher the risk of losing the volume of the real igneous bodies.</li>
	<li>Perform the operation with the provided software.
	<ol>
		<li>Click the Seismic Interpretation pane, click Insert a Horizon Probe. A probe will be added in the geobody interpretation probes tree of input pane. Double click the added horizon probe and a pop-up window will appear.</li>
		<li>Click the Horizons tab in the pop-up window and choose two seismic surfaces that isolate the zone of sills. Click OK to apply the operation.</li>
		<li>Check the newly added probe in the geobody interpretation probes tree shown in the input pane. A seismic cube will then appear in the 3D window.</li>
		<li>Double click the probe and choose the Opacity tab. A histogram of seismic amplitude will be shown in the tab. Use the left mouse button to draw a line in the histogram to control the opacity of the seismic cube. The low amplitude parts of the tube should be invisible and the high amplitude parts will be left.</li>
		<li>Adjust the histogram repeatedly until the desired shape of the interested geobody is achieved.</li>
	</ol>
	</li>
</ol>
4. Extraction of the Feeding Conduits
<ol>
	<li>Choose continuous and high energy reflection horizons at different depths beneath the surface lava flow.</li>
	<li>Do time slicing along the selected horizons, to find out discontinuities corresponding to the vertical conduits.</li>
	<li>Adjust the Two-Way Time (TWT) repeatedly, to achieve the best imaging of the discontinuities of the conduits. 
	NOTE: Seismic data cannot image vertical structures well, so better images from amplitude volumes and variance volumes are chosen by comparing clearness at different travel times.</li>
	<li>Try different slicing techniques, and then choose which can better image the discontinuities. 
	NOTE: Different tools can be used here, such as variance body slicing. Its theoretical basis is the similarity between each seismic section and adjacent seismic traces in the seismic data. Another tool, the variance cube, is a new data body processed by the conventional seismic data, which is helpful for the identification of changes in the structure and lithology, plane combination of the fault, etc.20</li>
	<li>Plot the slices at different travel times or depths into a 3D space.</li>
	<li>Perform the operation with the provided software.
	<ol>
		<li>Double click Volume Attributes in the geophysics tree of the processes pane. Check Structural Methods in the category column and Variance in the attribute column. Select the seismic cube to input box and adjust the other parameter in the parameter tab. For better reading performance, check the box in the realize column. A variance cube is created in the seismic tree of the input pane.</li>
		<li>Right click the variance cube and click Insert Time Slice Intersection to show more horizontal intersections in the 3D window. Use the Manipulate Plane tool in the toolbar of the 3D window to adjust the location of the slices to optimize the display of conduits.</li>
		<li>Right click the seismic amplitude cube and click Insert Time Slice Intersection to show more horizontal intersections in 3D window. Do the same operation as step 4.6.2 to adjust the location of the slices to optimize the display of conduits.</li>
	</ol>
	</li>
</ol>

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Soc. 169 (4), 421-426 (2012).</li><li>Thomson, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Volcanic+features+of+the+North+Rockall+Trough:+application+of+visualisation+techniques+on+3D+seismic+reflection+data.">Volcanic features of the North Rockall Trough: application of visualisation techniques on 3D seismic reflection data.</a> BVol. 67 (2), 116-128 (2005).</li><li>Jackson, C. A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Seismic+reflection+imaging+and+controls+on+the+preservation+of+ancient+sill-fed+magmatic+vents.">Seismic reflection imaging and controls on the preservation of ancient sill-fed magmatic vents.</a> J. Geol. Soc. 169 (5), 503-506 (2012).</li><li>Tian, W., 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+Tarim+picrite-basalt-rhyolite+suite,+a+Permian+flood+basalt+from+northwest+China+with+contrasting+rhyolites+produced+by+fractional+crystallization+and+anatexis.">The Tarim picrite-basalt-rhyolite suite, a Permian flood basalt from northwest China with contrasting rhyolites produced by fractional crystallization and anatexis.</a> CoMP. 160 (3), 407-425 (2010).</li><li>Chen, M. -. M., 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=Peridotite+and+pyroxenite+xenoliths+from+Tarim,+NW+China:+Evidences+for+melt+depletion+and+mantle+refertilization+in+the+mantle+source+region+of+the+Tarim+flood+basalt.">Peridotite and pyroxenite xenoliths from Tarim, NW China: Evidences for melt depletion and mantle refertilization in the mantle source region of the Tarim flood basalt.</a> Lithos. 204, 97-111 (2014).</li><li>Magee, C., Maharaj, S. M., Wrona, T., Jackson, C. A. 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The authors have nothing to disclose.

Here we demonstrate 2 methods for illustrating the morphology and structure of the plumbing system of buried basaltic volcanoes; one is opacity rendering, the other is time slicing.
The opacity rendering method is suitable for geo-bodies that have continuous and near horizontal interfaces with the encasing strata. With this method, one can extract the 3D morphology of magma lobes. Normally, flow directions should be along the long axis of the magma lobes. It is also important that the surface ...

The aim of most of the industrial seismic imaging projects in sedimentary basins is to explore for hydrocarbon reservoirs. In recent years, hydrocarbon exploration has expanded to basins containing large amounts of igneous rocks because many of the volcanogenic basins have considerable oil and gas reservoirs. However, because of the interface of igneous rocks in the volcanogenic basins, seismic data processing presents a series of challenges induced by various intrusions, such as reduced energy transmission, intrinsic attenuation, interference effects, refraction and scattering1. Therefore, oil field companies are focusing their efforts on reducing such a &#34;negative impact&#34; on seismic imaging2,3,4.
Igneous bodies within sedimentary basins are easily identified by two dimensional or 3D seismic reflection imaging due to the large acoustic impedance contrast with the encasing rocks1,5,6. This method can provide spectacular images of both vertical and horizontal structures of the volcanic plumbing systems7,8,9,10,11,12,13. However, the strategies of imaging subsurface volcanos are very different from that of oil and gas explorations8,14,15. This has limited the use of industrial seismic data in studies of subsurface volcanoes, apart from a few successful cases10,15,16. In this paper, we report detailed procedures of seismic data processing, which are customized for interpretation of subsurface volcanoes. We process two seismic cubes, TZ47 and YM2 (Figure 1), to show how to visualize the buried igneous bodies in the Tarim flood basalt17.

<table border="0" cellpadding="0" cellspacing="0" width="627">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">The Petrel E&#38;P software platform</td>
			<td style="width:125px;">Schlumberger</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">software version:2014</td>
		</tr>
	</tbody>
</table>

data processing methods for 3d seismic imaging of subsurface volcanoes: applications to the tarim flood basalt

The morphology and structure of plumbing systems can provide key information on the eruption rate and style of basalt lava fields. The most powerful way to study subsurface geo-bodies is to use industrial 3D&#160;reflection seismological imaging. However, strategies to image subsurface volcanoes are very different from that of oil and gas reservoirs. In this study, we process seismic data cubes from the Northern Tarim Basin, China, to illustrate how to visualize sills through opacity rendering techniques and how to image the conduits by time-slicing. In the first case, we isolated probes by the seismic horizons marking the contacts between sills and encasing strata, applying opacity rendering techniques to extract sills from the seismic cube. The resulting detailed sill morphology shows that the flow direction is from the dome center to the rim. In the second seismic cube, we use time-slices to image the conduits, which corresponds to marked discontinuities within the encasing rocks. A set of time-slices obtained at different depths show that the Tarim flood basalts erupted from central volcanoes, fed by separate pipe-like conduits.

We demonstrate the usefulness of the techniques described above by applying them to 2 types of igneous bodies, horizontal sills and vertical volcanic conduits. Extraction of the sills is conducted by using the opaque rendering technique, and interpretation of the volcanic conduit is performed by using slicing technique.
Extraction of sills
Industrial drilling wells have i...

Watch this Scientific Journal Video about Data Processing Methods for 3D Seismic Imaging of Subsurface Volcanoes: Applications to the Tarim Flood Basalt at JoVE.com

Data Processing Methods for 3D Seismic Imaging of Subsurface Volcanoes: Applications to the Tarim Flood Basalt

Three-dimensional (3D) reflection seismology is a powerful method for imaging subsurface volcanoes. By using industrial 3D seismological data from the Tarim Basin, we illustrate how to extract the sills and the conduits of subsurface volcanoes from seismic data cubes.

The morphology and structure of plumbing systems can provide key information on the eruption rate and style of basalt lava fields. The most powerful way ...

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9.2K Views.  Peking University. Three-dimensional (3D) reflection seismology is a powerful method for imaging subsurface volcanoes. By using industrial 3D seismological data from the Tarim Basin, we illustrate how to extract the sills and the conduits of subsurface volcanoes from seismic data cubes.

Video: Data Processing Methods for 3D Seismic Imaging of Subsurface Volcanoes: Applications to the Tarim Flood Basalt

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced 1,2 and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production 3 and developed systems for both transient and stable transformation 4. However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses.
The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 &deg;C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

We have developed a methodology for performing crosses in Setaria viridis (S. viridis). The method involves pruning the panicle prior to a hot water treatment to kill viable pollen. Crosses are performed following a well-controlled growth regime and typically result in the recovery of 1 to 7 cross-pollinated seed/s per panicle.

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail ...

Surface Renewal: An Advanced Micrometeorological Method for Measuring and Processing Field-Scale Energy Flux Density Data

Advanced micrometeorological methods have become increasingly important in soil, crop, and environmental sciences. For many scientists without formal training in atmospheric science, these techniques are relatively inaccessible. Surface renewal and other flux measurement methods require an understanding of boundary layer meteorology and extensive training in instrumentation and multiple data management programs. To improve accessibility of these techniques, we describe the underlying theory of surface renewal measurements, demonstrate how to set up a field station for surface renewal with eddy covariance calibration, and utilize our open-source turnkey data logger program to perform flux data acquisition and processing. The new turnkey program returns to the user a simple data table with the corrected fluxes and quality control parameters, and eliminates the need for researchers to shuttle between multiple processing programs to obtain the final flux data. An example of data generated from these measurements demonstrates how crop water use is measured with this technique. The output information is useful to growers for making irrigation decisions in a variety of agricultural ecosystems. These stations are currently deployed in numerous field experiments by researchers in our group and the California Department of Water Resources in the following crops: rice, wine and raisin grape vineyards, alfalfa, almond, walnut, peach, lemon, avocado, and corn.

Surface renewal is a micrometeorological method that is being used increasingly to determine energy fluxes, but its technical complexity makes it inaccessible to a broad audience. We describe the steps needed to set up and calibrate a surface renewal field station, to acquire and process data, and to correctly interpret results.

Advanced micrometeorological methods have become  increasingly important in soil, crop, and environmental sciences.  For many scientists without formal ...

Exploring the Effects of Atmospheric Forcings on Evaporation: Experimental Integration of the Atmospheric Boundary Layer and Shallow Subsurface

Evaporation is directly influenced by the interactions between the atmosphere, land surface and soil subsurface. This work aims to experimentally study evaporation under various surface boundary conditions to improve our current understanding and characterization of this multiphase phenomenon as well as to validate numerical heat and mass transfer theories that couple Navier-Stokes flow in the atmosphere and Darcian flow in the porous media. Experimental data were collected using a unique soil tank apparatus interfaced with a small climate controlled wind tunnel. The experimental apparatus was instrumented with a suite of state of the art sensor technologies for the continuous and autonomous collection of soil moisture, soil thermal properties, soil and air temperature, relative humidity, and wind speed. This experimental apparatus can be used to generate data under well controlled boundary conditions, allowing for better control and gathering of accurate data at scales of interest not feasible in the field. Induced airflow at several distinct wind speeds over the soil surface resulted in unique behavior of heat and mass transfer during the different evaporative stages.

A protocol for the design and construction of a soil tank interfaced to a small climate controlled wind tunnel to study the effects of atmospheric forcings on evaporation is presented. Both the soil tank and wind tunnel are instrumented with sensor technologies for the continuous in situ measurement of environmental conditions.

Evaporation is directly influenced by the interactions between the atmosphere, land surface and soil subsurface. This work aims to experimentally study ...

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 ...

Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental changes. Repeated sampling to monitor these changes in forest soils is a relatively new practice that is not well documented in the literature and has only recently been broadly embraced by the scientific community. The objective of this protocol is therefore to synthesize the latest information on methods of soil resampling in a format that can be used to design and implement a soil monitoring program. Successful monitoring of forest soils requires that a study unit be defined within an area of forested land that can be characterized with replicate sampling locations. A resampling interval of 5 years is recommended, but if monitoring is done to evaluate a specific environmental driver, the rate of change expected in that driver should be taken into consideration. Here, we show that the sampling of the profile can be done by horizon where boundaries can be clearly identified and horizons are sufficiently thick to remove soil without contamination from horizons above or below. Otherwise, sampling can be done by depth interval. Archiving of sample for future reanalysis is a key step in avoiding analytical bias and providing the opportunity for additional analyses as new questions arise.

Repeated soil sampling has recently been shown to be an effective way to monitor forest soil change over years and decades. To support its use, a protocol is presented that synthesizes the latest information on soil resampling methods to aid in the design and implementation of successful soil monitoring programs.

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental ...

Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and estimating fish abundance. We developed and implemented a rotating stereo-video camera tool that covers a full 360 degrees of sampling, which maximizes sampling effort compared to stationary camera tools. A variety of studies have detailed the ability of static, stereo-camera systems to obtain highly accurate and precise measurements of fish; the focus here was on the development of methodological approaches to quantify fish density using rotating camera systems. The first approach was to develop a modification of the metric MaxN, which typically is a conservative count of the minimum number of fish observed on a given camera survey. We redefine MaxN to be the maximum number of fish observed in any given rotation of the camera system. When precautions are taken to avoid double counting, this method for MaxN may more accurately reflect true abundance than that obtained from a fixed camera. Secondly, because stereo-video allows fish to be mapped in three-dimensional space, precise estimates of the distance-from-camera can be obtained for each fish. By using the 95% percentile of the observed distance from camera to establish species-specific areas surveyed, we account for differences in detectability among species while avoiding diluting density estimates by using the maximum distance a species was observed. Accounting for this range of detectability is critical to accurately estimate fish abundances. This methodology will facilitate the integration of rotating stereo-video tools in both applied science and management contexts.

We describe a new method for counting fishes, and estimating relative abundance (MaxN) and fish density using rotating stereo-video camera systems. We also demonstrate how to use distance from camera (Z distance) to estimate species-specific detectability.

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and ...

Experimental Methods of Dust Charging and Mobilization on Surfaces with Exposure to Ultraviolet Radiation or Plasmas

Electrostatic dust transport has been hypothesized to explain a number of observations of unusual planetary phenomena. Here, it is demonstrated using three recently developed experiments in which dust particles are exposed to thermal plasma with beam electrons, beam electrons only, or ultraviolet (UV) radiation only. The UV light source has a narrow bandwidth in wavelength centered at 172 nm. The beam electrons with the energy of 120 eV are created with a negatively biased hot filament. When the vacuum chamber is filled with the argon gas, a thermal plasma is created in addition to the electron beam. Insulating dust particles of a few tens of microns in diameter are used in the experiments. Dust particles are recorded to be lofted to a height up to a few centimeters with a launch speed up to 1 m/s. These experiments demonstrate that photo and/or secondary electron emission from a dusty surface changes the charging mechanism of dust particles. According to the recently developed &#34;patched charge model&#34;, the emitted electrons can be re-absorbed inside microcavities between neighboring dust particles below the surface, causing the accumulation of enhanced negative charges on the surrounding dust particles. The repulsive forces between these negatively charged particles may be large enough to mobilize and lift them off the surface. These experiments present the advanced understanding of dust charging and transport on dusty surfaces, and laid a foundation for future investigations of its role in the surface evolution of airless planetary bodies.

Dust charging and mobilization is demonstrated in three experiments with exposure to thermal plasma with beam electrons, beam electrons only, or ultraviolet (UV) radiation only. These experiments present the advanced understanding of electrostatic dust transport and its role in shaping the surfaces of airless planetary bodies.

Electrostatic dust transport has been hypothesized to explain a number of observations of unusual planetary phenomena. Here, it is demonstrated using ...

Harvesting Venom Toxins from Assassin Bugs and Other Heteropteran Insects

Heteropteran insects such as assassin bugs (Reduviidae) and giant water bugs (Belostomatidae) descended from a common predaceous and venomous ancestor, and the majority of extant heteropterans retain this trophic strategy. Some heteropterans have transitioned to feeding on vertebrate blood (such as the kissing bugs, Triatominae; and bed bugs, Cimicidae) while others have reverted to feeding on plants (most Pentatomomorpha). However, with the exception of saliva used by kissing bugs to facilitate blood-feeding, little is known about heteropteran venoms compared to the venoms of spiders, scorpions and snakes.
One obstacle to the characterization of heteropteran venom toxins is the structure and function of the venom/labial glands, which are both morphologically complex and perform multiple biological roles (defense, prey capture, and extra-oral digestion). In this article, we describe three methods we have successfully used to collect heteropteran venoms. First, we present electrostimulation as a convenient way to collect venom that is often lethal when injected into prey animals, and which obviates contamination by glandular tissue. Second, we show that gentle harassment of animals is sufficient to produce venom extrusion from the proboscis and/or venom spitting in some groups of heteropterans. Third, we describe methods to harvest venom toxins by dissection of anaesthetized animals to obtain the venom glands. This method is complementary to other methods, as it may allow harvesting of toxins from taxa in which electrostimulation and harassment are ineffective. These protocols will enable researchers to harvest toxins from heteropteran insects for structure-function characterization and possible applications in medicine and agriculture.

Although many insects in the suborder Heteroptera (Insecta: Hemiptera) are venomous, their venom composition and the functions of their venom toxins are mostly unknown. This protocol describes methods to harvest heteropteran venoms for further characterization, using electrostimulation, harassment, and gland dissection.

Heteropteran insects such as assassin bugs (Reduviidae) and giant water bugs (Belostomatidae) descended from a common predaceous and venomous ancestor, ...

Composition and Distribution Analysis of Bioaerosols Under Different Environmental Conditions

Variable microorganisms in particulate matter (PM) under different environmental conditions may have significant impacts on human health. In this study, we described a protocol for multiple analyses of the biological compositions in environmental PM. Five experiments are presented: (1) PM number monitoring by using a laser particle counter; (2) PM collection by using a cyclonic aerosol sampler; (3) PM collection by using a high-volume air sampler with filters; (4) culturable microbes collection by the Andersen six-stage sampler; and (5) detection of biological composition of environmental PM by bacterial 16SrDNA and fungal ITS region sequencing. We selected hazy days and a livestock farm as two typical examples of the application in this protocol. In this study, these two sampling methods, cyclonic aerosol sampler and filter sampler, showed different sampling efficiency. The cyclonic aerosol sampler performed much better in terms of collecting bacteria, while these two methods showed the same efficiency in collecting fungi. Filter samplers can work under low temperature conditions while cyclonic aerosol samplers have a sampling limitation for temperature. A solid impacting sampler, such as an Andersen six-stage sampler, can be used to sample bioaerosols directly into the culture medium, which increases the survival rate of culturable microorganisms. However, this method mainly relies on culture while more than 99% of microbes cannot be cultured. DNA extracted from the culturable bacteria collected by the Andersen six-stage sampler and samples collected by cyclonic aerosol sampler and filter sampler were detected by bacterial 16S rDNA and fungal ITS region sequencing.All the methods above may have wide application in many fields of study, such as environmental monitoring and airborne pathogen detection. From these results, we can conclude that these methods can be used under different conditions and may help other researchers further explore the health impacts of environmental bioaerosols.

Understanding the biological composition of environmental particulate matter is important for the study of its significant impacts on human health and disease spread. Here, we used three types of bioaerosol sampling methods and a biological analysis of airborne microbes to better explore airborne microbial communities under different environmental conditions.

Variable microorganisms in particulate matter (PM) under different environmental conditions may have significant impacts on human health. In this study, ...

Processing Embryo, Eggshell, and Fungal Culture for Scanning Electron Microscopy

Although scanning electron microscopy (SEM) is being widely used for the ultra-structural analysis of various biological and non-biological samples, methods involved in processing different biological samples involve unique practices. All conventional practices described in the literature for processing samples still find useful applications, but subtle changes in the sample preparation can alter image quality, as well as, introduce artifacts. Hence, using a unique sample preparation technique specific to the type of tissue analyzed is required to obtain a good quality image with ultrastructural resolution. The focus of this study is to provide the optimal sample preparation protocols for imaging embryos, rigid eggshells, and fungal cultures using SEM. The following optimizations were recommended to yield good results for the three different delicate biological samples studied. Use of milder fixatives like 4% paraformaldehyde or 3% glutaraldehyde followed by dehydration with ethanol series is mandatory. Fungal mycelium on agar blocks obtained by slide cultures yields a better ultrastructural integrity compared to cultures taken directly from agar plates. Chemical drying of embryos with HMDS provides drying without introducing surface tension artifacts compared to critical point drying. HMDS prevents cracking caused by shrinkage as samples are less brittle during drying. However, for fungal culture, critical point drying provides acceptable image quality compared to chemical drying. Eggshells can be imaged with no special preparation steps except for thorough washing and air drying prior to mounting. Preparation methodologies were standardized based on acceptable image quality obtained with each trial.&#160;

Here, we present detailed processing protocols for imaging delicate tissue samples using scanning electron microscopy (SEM). Three different processing methods, namely, hexamethyl disilazana (HMDS) chemical drying, simple air drying, and critical point drying are described for preparing rigid eggshells, embryos at early developmental stages, and fungal cultures respectively.

Although scanning electron microscopy (SEM) is being widely used for the ultra-structural analysis of various biological and non-biological samples, ...