Name: construction of a compact low-cost radiation shield for air-temperature sensors in ecological field studies
Uploaded: 2018-11-06T13:00:00
Description: Watch this Scientific Journal Video about Construction of a Compact Low-Cost Radiation Shield for Air-Temperature Sensors in Ecological Field Studies at JoVE.com

We thank Emily Meineke for contributions to the original study design and experiment. We thank Ryan Boyles for facilitating access to the study sites and weather-station data. Jaime Collazo, Steven Frank, and Erica Henry provided the data loggers and radiation shields. Access to study site was approved by the North Carolina State Climate Office. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

1. Construction of the Radiation Shield
<ol>
	<li>Using a utility knife, cut the corrugated plastic sheets into squares (Figure 1A). One 15 cm square and two 10 cm squares will be needed for each shield.</li>
	<li>Cuts for the top layer of the small radiation shield (Figure 1B; left image):
	<ol>
		<li>On the 15 cm square, measure 4 cm from one edge and draw a line with a pencil. Use a straightedge as a guide to score along the line. (Herein, &#8220;scoring&#8...

<ol>
	<li>Bowker, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anurans,+the+group+of+terrestrial+vertebrates+most+vulnerable+to+climate+change:+A+case+study+with+acoustic+monitoring+in+the+Iberian+peninsula.">Anurans, the group of terrestrial vertebrates most vulnerable to climate change: A case study with acoustic monitoring in the Iberian peninsula.</a> Computational bioacoustics for assessing biodiversity. , 43 (2007).</li><li>Walther, G. -. R., 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=Ecological+responses+to+recent+climate+change.">Ecological responses to recent climate change.</a> Nature. 416 (6879), 389-395 (2002).</li><li>Inouye, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+climate+change+on+phenology,+frost+damage,+and+floral+abundance+of+montane+wildflowers.">Effects of climate change on phenology, frost damage, and floral abundance of montane wildflowers.</a> Ecology. 89 (2), 353-362 (2008).</li><li>Lundquist, J. D., Huggett, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evergreen+trees+as+inexpensive+radiation+shields+for+temperature+sensors.">Evergreen trees as inexpensive radiation shields for temperature sensors.</a> Water Resources Research. 44 (4), W00D04 (2008).</li><li>De Jong, S. A. P., Slingerland, J. D., Van De Giesen, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiber+optic+distributed+temperature+sensing+for+the+determination+of+air+temperature.">Fiber optic distributed temperature sensing for the determination of air temperature.</a> Atmospheric Measurement Techniques. 8 (1), 335-339 (2015).</li><li>Holden, Z. A., Klene, A. E., Keefe, R. F., Moisen, G. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+evaluation+of+an+inexpensive+radiation+shield+for+monitoring+surface+air+temperatures.">Design and evaluation of an inexpensive radiation shield for monitoring surface air temperatures.</a> Agricultural and Forest Meteorology. 180, 281-286 (2013).</li><li>Terando, A. J., Youngsteadt, E., Meineke, E. K., Prado, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ad+hoc+instrumentation+methods+in+ecological+studies+produce+highly+biased+temperature+measurements.">Ad hoc instrumentation methods in ecological studies produce highly biased temperature measurements.</a> Ecology and Evolution. 7 (23), 9890-9904 (2017).</li><li>Richardson, S. J., 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=Minimizing+errors+associated+with+multiplate+radiation+shields.">Minimizing errors associated with multiplate radiation shields.</a> Journal of Atmospheric and Oceanic Technology. 16 (11), 1862-1872 (1999).</li><li>Anderson, S. P., Baumgartner, M. F., Anderson, S. P., Baumgartner, M. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Radiative+Heating+Errors+in+Naturally+Ventilated+Air+Temperature+Measurements+Made+from+Buoys.">Radiative Heating Errors in Naturally Ventilated Air Temperature Measurements Made from Buoys.</a> Journal of Atmospheric and Oceanic Technology. 15 (1), 157-173 (1998).</li><li>Nakamura, R., Mahrt, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Air+temperature+measurement+errors+in+naturally+ventilated+radiation+shields.">Air temperature measurement errors in naturally ventilated radiation shields.</a> Journal of Atmospheric and Oceanic Technology. 22 (7), 1046-1058 (2005).</li><li>Tarara, J. M., Hoheisel, 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=Low-cost+shielding+to+minimize+radiation+errors+of+temperature+sensors+in+the+field.">Low-cost shielding to minimize radiation errors of temperature sensors in the field.</a> HortScience. 42 (6), 1372-1379 (2007).</li><li>Huwald, H., Higgins, C. W., Boldi, M. -. O., Bou-Zeid, E., Lehning, M., Parlange, 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=Albedo+effect+on+radiative+errors+in+air+temperature+measurements.">Albedo effect on radiative errors in air temperature measurements.</a> Water Resources Research. 45 (8), (2009).</li><li>Fuchs, M., Tanner, C. 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The accuracy and repeatability of air temperature measurements depend on the use of an appropriate solar shield that protects the sensor from direct and reflected solar radiation. Here we describe the construction of such a shield that is more compact in size, less expensive, or faster to construct than similar, previously described devices6, without sacrificing accuracy. 94% of the recorded temperatures for the thermochrons outfitted with the smaller shield were within 1.0 &#176;C of the best per...

In light of anthropogenic global warming, there has been a growing interest in recording air temperature in a variety of settings to understand and predict ecological responses to climate change1,2,3. With the advent of small, low-cost environmental data recorders (also referred to as data loggers, thermochrons, or hygrochrons), it is now possible to deploy high-density networks of sensors to measure hyper localized temperature variation, increasing ecologists&#39; ability to more directly observe the ambient environmental conditions experienced by organisms and ecosystems under study. Compared to existing, well-calibrated and rigorously tested&#8212;but sparsely distributed&#8212;permanent weather stations, such networks present opportunities to assess climatic variation on ecologically relevant scales but may reduce accuracy or comparability among studies if inconsistently or inappropriately deployed.
Near-surface air temperature sensors typically require some type of solar radiation shielding to prevent direct heating of the sensor element, which would result in erroneously warm measurements. Common ways to limit sensor bias include: 1) using existing environmental features such as trees for shading4, 2) bias correction and sensor calibration5 that derived corrections based on the thermal properties of sensors, and 3) the use of manufactured or custom fabricated shields6,7. Many researchers choose to use custom fabricated shields because of the low-cost and easy deployment, and necessity in situations where environmental conditions do not provide natural shading. However, a review of the ecological literature indicated that the design of custom fabricated shields varies widely among studies, and individual designs are rarely tested for accuracy. Untested shields can be susceptible to poor choice of materials and design that cause additional heating of the air molecules immediately surrounding the sensor, direct absorption of solar radiation by the sensor itself, or both-leading to average biases of up to 3 &#176;C7. On the other hand, simple and cost-effective designs6,7 are quite effective at shielding sensors (biases of 1 &#176;C or less) and are comparable to commercially manufactured radiation shields.
Here, we provide a detailed methodology for constructing a previously evaluated custom fabricated radiation shield7 for use with inexpensive thermochron temperature sensors. The shield design is a modification of one previously described and tested in an open Ponderosa Pine forest setting6. In recent tests of several custom-fabricated shield designs, this montane-tested shield resulted in the lowest biases when paired with small thermochrons7, but we found it cumbersome and too conspicuous to deploy in the field. The design protocol proposed here reduces the dimensions of the radiation shield by 50%. Such a reduction in size has several benefits: 1) it is less conspicuous and therefore less susceptible to tampering, 2) it can be more feasibly used in a wider variety of ecological settings where space is limited (e.g., on smaller urban street trees), 3) it is more accurate than other published shielding methods that attempt to minimize shield size or construction costs7, and 4) it is less expensive than the original, larger design due to the reduced quantity of construction materials required. After describing the construction methods, we explore the effect of the size reduction on sensor accuracy relative to the original shield design using results from a field trial conducted under high downward solar radiation conditions.

<table>
	<tbody>
		<tr>
			<td>Multipurpose Aluminum Foil Tape</td>
			<td>Nashua</td>
			<td>1087671</td>
			<td>48 mm width</td>
		</tr>
		<tr>
			<td>8&#34; cable ties</td>
			<td>DTOL</td>
			<td>GEN86371</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Corrugated plastic sheet&#160;</td>
			<td>Highway Traffic supply</td>
			<td>hts18X24COROW</td>
			<td>White sheet 18&#34;L x 24&#34;W, 5-pack</td>
		</tr>
		<tr>
			<td>Standard utility knife</td>
			<td>NA</td>
			<td>NA</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Standard Scissors</td>
			<td>NA</td>
			<td>NA</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Heavy duty stapler</td>
			<td>Swingline</td>
			<td>552277715</td>
			<td>NA</td>
		</tr>
	</tbody>
</table>

construction of a compact low-cost radiation shield for air-temperature sensors in ecological field studies

Low cost temperature sensors are increasingly used by ecologists to assess climatic variation and change on ecologically relevant scales. Although cost-effective, if not deployed with proper solar radiation shielding, the observations recorded from these sensors will be biased and inaccurate. Manufactured radiation shields are effective at minimizing this bias, but are expensive compared to the cost of these sensors. Here, we provide a detailed methodology for constructing a compact version of a previously described custom fabricated radiation shield, which is more accurate than other published shielding methods that attempt to minimize shield size or construction costs. The method requires very little material: corrugated plastic sheets, aluminum foil duct tape, and cable ties. One 15 cm and two 10 cm squares of corrugated plastic are used for each shield. After cutting, scoring, taping and stapling of the sheets, the 10 cm squares form the bottom two layers of the solar radiation shield, while the 15 cm square forms the top layer. The three sheets are held together with cable ties. This compact solar radiation shield can be suspended, or placed against any flat surface. Care must be taken to ensure that the shield is completely parallel to the ground to prevent direct solar radiation from reaching the sensor, possibly causing increased warm biases in sun-exposed sites in the morning and afternoon relative to the original, larger design. Even so, differences in recorded temperatures between the smaller, compact shield design and the original design were small (mean daytime bias = 0.06 &#176;C). Construction costs are less than half of the original shield design, and the new design results in a less conspicuous instrument that may be advantageous in many field ecology settings.

Representative results using thermochrons outfitted with the new, smaller shield design, the original larger shield design, and the thermochrons with no radiation shield are shown in Figure 2 and Figure 3. These data were recorded at a fully exposed rural location near Raleigh, NC (35.728&#176;N, 78.680&#176;W), and were affixed to a well-calibrated permanent weather station outfitted with a VAISALA platinum resi...

Watch this Scientific Journal Video about Construction of a Compact Low-Cost Radiation Shield for Air-Temperature Sensors in Ecological Field Studies at JoVE.com

Construction of a Compact Low-Cost Radiation Shield for Air-Temperature Sensors in Ecological Field Studies

With the advent of small, low-cost environmental sensors, it is now possible to deploy high-density networks of sensors to measure hyper localized temperature variation. Here, we provide a detailed methodology for constructing a compact version of a previously described custom-fabricated radiation shield for use with inexpensive thermochrons.

Low cost temperature sensors are increasingly used by ecologists to assess climatic variation and change on ecologically relevant scales. Although ...

This method for constructing a low-cost radiation shield can help improve air temperature measurements in ecological field studies. The main advantage of this technique is the small size of the shield which reduces construction cost to less than half that of similar models and makes your instruments less conspicuous in the field. To construct a radiation shield use a utility knife to cut corrugated plastic sheets into one 15 centimeter and two 10 centimeter squares.For the top layer of the small radiation shield, use a pencil to draw a line four centimeters from one edge of the 15 centimeter square and use a straight edge as a guide to score along the line. Next, measure 3.8 centimeters from the edges perpendicular to the four centimeter line, and use the straight edge to score from the bottom of the square up to the four centimeter line. Then draw a line from both corners above the four centimeter line to the junction of the four centimeter and 3.8 centimeter lines, and cut along this line.For the middle and bottom layers of the small radiation shield, use the straight edge to draw a six centimeter square in the middle of each 10 centimeter square, and score all around each six centimeter square, and from each corner of the six centimeter squares to the outer corners of the 10 centimeter squares. Now, fold the 15 centimeter sheet along the scored lines, and tuck the small triangular flaps on the inside of the larger back flap, securing temporarily with binder clips, and completely cover the scored side with aluminum foil tape. When the 15 centimeter square is folded correctly, the cut edge of the back flap will be flush with the folded sides, and the entire convex surface will be taped.Then use aluminum foil tape to completely cover the scored side of one of the 10 centimeter squares, and the unscored side of the other 10 centimeter square. Using a 1/4 inch drill bit, drill holes in each of the shields'layers, and run a cable tie through the eyelet of the censor housing and through the holes of the underside of the 10 centimeter square that is taped on the scored side and has the two holes drilled into the middle. Pinch the sides of each 10 centimeter square along its diagonal scored lines, using a heavy duty stapler to hold the pinched sides together.The end product will have a square bowl shape. When the second bowl is finished, thread a cable tie first through the left back hole of the 10 centimeter sheet taped on the unscored side. Then, through the left back hole of the second 10 centimeter sheet, leaving a two centimeter vertical space between the two sheets to allow airflow around the temperature censor.Thread a cable through the back right holes in the same way, and pass a cable tie through the two side by side holes in the back left of the 15 centimeter square sheet. Attach this tie to the 10 centimeter sheets, leaving two centimeter of space between the 15 centimeter sheet and the top of the upper 10 centimeter sheet, and thread the two side by side holes in the back right of the 15 centimeter sheet in the same manner. For mounting, drill additional holes into the back end of the assembled product as necessary.Then pass one cable tie through all three holes in the front of the sheets, and tighten the cable tie, taking care that the space is even between all three sheets. Ensure that the three sheets lay parallel to the ground when mounted. In this representative field experiment, positive biases were found across all four tested censors using the small radiation shield that were similar to those obtained using the original larger shield design, but were much less than the biases of the unshielded censors.The small shields also resulted in the recording of some outlier warm temperatures relative to the original shield design, although the overall differences were small. Warm biases were strongest during periods of peak solar radiation, but in both the small and large shield cases, these biases were much less than the biases of the unshielded censors. The mean temperature differences between all of the combinations of censors outfitted with the small radiation shield compared to the original design, revealed that the largest differences occurred at 08:00 hours local time.When constructing this shield, it's important to remember to completely cover each square with the reflective aluminum tape, to keep even spacing between the squares, and to mount the final constructed shield parallel to the ground. Measuring microclimatic variation in air temperature can help provide insights into local biological responses to recent and projected climate change. Using a radiation shield with well documented properties can help ensure meaningful comparisons between studies.

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Environment

Physical, Chemical and Biological Characterization of Six Biochars Produced for the Remediation of Contaminated Sites

The physical and chemical properties of biochar vary based on feedstock sources and production conditions, making it possible to engineer biochars with specific functions (e.g. carbon sequestration, soil quality improvements, or contaminant sorption). In 2013, the International Biochar Initiative (IBI) made publically available their Standardized Product Definition and Product Testing Guidelines (Version 1.1) which set standards for physical and chemical characteristics for biochar. Six biochars made from three different feedstocks and at two temperatures were analyzed for characteristics related to their use as a soil amendment. The protocol describes analyses of the feedstocks and biochars and includes: cation exchange capacity (CEC), specific surface area (SSA), organic carbon (OC) and moisture percentage, pH, particle size distribution, and proximate and ultimate analysis. Also described in the protocol are the analyses of the feedstocks and biochars for contaminants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), metals and mercury as well as nutrients (phosphorous, nitrite and nitrate and ammonium as nitrogen). The protocol also includes the biological testing procedures, earthworm avoidance and germination assays. Based on the quality assurance / quality control (QA/QC) results of blanks, duplicates, standards and reference materials, all methods were determined adequate for use with biochar and feedstock materials. All biochars and feedstocks were well within the criterion set by the IBI and there were little differences among biochars, except in the case of the biochar produced from construction waste materials. This biochar (referred to as Old biochar) was determined to have elevated levels of arsenic, chromium, copper, and lead, and failed the earthworm avoidance and germination assays. Based on these results, Old biochar would not be appropriate for use as a soil amendment for carbon sequestration, substrate quality improvements or remediation.

Biochar is a carbon-rich material used as a soil amendment with the ability to sustainably sequester carbon, improve substrate quality and sorb contaminants. This protocol describes the 17 analytical methods used for the characterization of biochar, which is required prior to large scale implementation of these amendments in the environment.

The physical and chemical properties of biochar vary based on feedstock sources and production conditions, making it possible to engineer biochars with ...

Pretreatment of Lignocellulosic Biomass with Low-cost Ionic Liquids

A number of ionic liquids (ILs) with economically attractive production costs have recently received growing interest as media for the delignification of a variety of lignocellulosic feedstocks. Here we demonstrate the use of these low-cost protic ILs in the deconstruction of lignocellulosic biomass (Ionosolv pretreatment), yielding cellulose and a purified lignin. In the most generic process, the protic ionic liquid is synthesized by accurate combination of aqueous acid and amine base. The water content is adjusted subsequently. For the delignification, the biomass is placed into a vessel with IL solution at elevated temperatures to dissolve the lignin and hemicellulose, leaving a cellulose-rich pulp ready for saccharification (hydrolysis to fermentable sugars). The lignin is later precipitated from the IL by the addition of water and recovered as a solid. The removal of the added water regenerates the ionic liquid, which can be reused multiple times. This protocol is useful to investigate the significant potential of protic ILs for use in commercial biomass pretreatment/lignin fractionation for producing biofuels or renewable chemicals and materials.

The pretreatment of lignocellulosic biomass with protic low-cost ionic liquids is shown, resulting in a delignified cellulose-rich pulp and a purified lignin. The pulp gives rise to high glucose yields after enzymatic saccharification.

A number of ionic liquids (ILs) with economically attractive production costs have recently received growing interest as media for the delignification of ...

Measuring the Flight Ability of the Ambrosia Beetle, Platypus Quercivorus (Murayama), Using a Low-Cost, Small, and Easily Constructed Flight Mill

The ambrosia beetle, Platypus quercivorus (Murayama), is the vector of a fungal pathogen that causes mass mortality of Fagaceae trees (Japanese oak wilt). Therefore, knowing the dispersal capacity may help inform trapping/tree removal efforts to prevent this disease more effectively. In this study, we measured the flight velocity and duration and estimated the flight distance of the beetle using a newly developed flight mill. The flight mill is low cost, small, and constructed using commonly available items. Both the flight mill arm and its vertical axis comprise a thin needle. A beetle specimen is glued to one tip of the arm using instant glue. The other tip is thick due to being covered with plastic, thus it facilitates the detection of rotations of the arm. The revolution of the arm is detected by a photo sensor mounted on an infrared LED, and is indicated by a change in the output voltage when the arm passed above the LED. The photo sensor is connected to a personal computer and the output voltage data are stored at a sampling rate of 1 kHz. By conducting experiments using this flight mill, we found that P. quercivorus can fly at least 27 km. Because our flight mill comprises cheap and small ordinary items, many flight mills can be prepared and used simultaneously in a small laboratory space. This enables experimenters to obtain a sufficient amount of data within a short period.

Measuring the Flight Ability of the Ambrosia Beetle, Platypus Quercivorus Murayama, Using a Low-Cost, Small, and Easily Constructed Flight Mill

We developed a low cost and small flight mill, constructed with commonly available items and easily used in experimentation. Using this apparatus, we measured the flight ability of an ambrosia beetle, Platypus quercivorus.

The ambrosia beetle, Platypus quercivorus (Murayama), is the vector of a fungal pathogen that causes mass mortality of Fagaceae trees (Japanese oak wilt). ...

A Flexible Low Cost Hydroponic System for Assessing Plant Responses to Small Molecules in Sterile Conditions

A wide range of studies in plant biology are performed using hydroponic cultures. In this work, an in vitro hydroponic growth system designed for assessing plant responses to chemicals and other substances of interest is presented. This system is highly efficient in obtaining homogeneous and healthy seedlings of the C3 and C4 model species Arabidopsis thaliana and Setaria viridis, respectively. The sterile cultivation avoids algae and microorganism contamination, which are known limiting factors for plant normal growth and development in hydroponics. In addition, this system is scalable, enabling the harvest of plant material on a large scale with minor mechanical damage, as well as the harvest of individual parts of a plant if desired. A detailed protocol demonstrating that this system has an easy and low-cost assembly, as it uses pipette racks as the main platform for growing plants, is provided. The feasibility of this system was validated using Arabidopsis seedlings to assess the effect of the drug AZD-8055, a chemical inhibitor of the target of rapamycin (TOR) kinase. TOR inhibition was efficiently detected as early as 30 min after an AZD-8055 treatment in roots and shoots. Furthermore, AZD-8055-treated plants displayed the expected starch-excess phenotype. We proposed this hydroponic system as an ideal method for plant researchers aiming to monitor the action of plant inducers or inhibitors, as well as to assess metabolic fluxes using isotope-labeling compounds which, in general, requires the use of expensive reagents.

A simple, versatile, and low-cost in vitro hydroponic system was successfully optimized, enabling large-scale experiments under sterile conditions. This system facilitates the application of chemicals in a solution and their efficient absorption by roots for molecular, biochemical, and physiological studies.

A wide range of studies in plant biology are performed using hydroponic cultures. In this work, an in vitro hydroponic growth system designed for ...

Experimental Protocol for Examining Behavioral Response Profiles in Larval Fish: Application to the Neuro-stimulant Caffeine

Fish models and behaviors are increasingly used in the biomedical sciences; however, fish have long been the subject of ecological, physiological and toxicological studies. Using automated digital tracking platforms, recent efforts in neuropharmacology are leveraging larval fish locomotor behaviors to identify potential therapeutic targets for novel small molecules. Similar to these efforts, research in the environmental sciences and comparative pharmacology and toxicology is examining various behaviors of fish models as diagnostic tools in tiered evaluation of contaminants and real-time monitoring of surface waters for contaminant threats. Whereas the zebrafish is a popular larval fish model in the biomedical sciences, the fathead minnow is a common larval fish model in ecotoxicology. Unfortunately, fathead minnow larvae have received considerably less attention in behavioral studies. Here, we develop and demonstrate a behavioral profile protocol using caffeine as a model neurostimulant. Though photomotor responses of fathead minnows were occasionally affected by caffeine, zebrafish&#160;were markedly more sensitive for photomotor and locomotor endpoints, which responded at environmentally relevant levels. Future studies are needed to understand comparative behavioral sensitivity differences among fish with age and time of day, and to determine whether similar behavioral effects would occur in nature and be indicative of adverse outcomes at the individual or population levels of biological organization.

Here, we present a protocol to examine larval zebrafish and fathead minnow locomotor activities and photomotor responses (PMR) using an automated tracking software. When incorporated in common toxicology bioassays, analyses of these behaviors provide a diagnostic tool to examine chemical bioactivity. This protocol is described using caffeine, a model neurostimulant.

Fish models and behaviors are increasingly used in the biomedical sciences; however, fish have long been the subject of ecological, physiological and ...

Construction of a Low-cost Mobile Incubator for Field and Laboratory Use

Incubators are essential for a range of culture-based microbial methods, such as membrane filtration followed by cultivation for assessing drinking water quality. However, commercially available incubators are often costly, difficult to transport, not flexible in terms of volume, and/or poorly adapted to local field conditions where access to electricity is unreliable. The purpose of this study was to develop an adaptable, low-cost and transportable incubator that can be constructed using readily available components. The electronic core of the incubator was first developed. These components were then tested under a range of ambient temperature conditions (3.5 &#176;C - 39 &#176;C) using three types of incubator shells (polystyrene foam box, hard cooler box, and cardboard box covered with a survival blanket). The electronic core showed comparable performance to a standard laboratory incubator in terms of the time required to reach the set temperature, inner temperature stability and spatial dispersion, power consumption, and microbial growth. The incubator set-ups were also effective at moderate and low ambient temperatures (between 3.5 &#176;C and 27 &#176;C), and at high temperatures (39 &#176;C) when the incubator set temperature was higher. This incubator prototype is low-cost (&lt; 300 USD) and adaptable to a variety of materials and volumes. Its demountable structure makes it easy to transport. It can be used in both established laboratories with grid power or in remote settings powered by solar energy or a car battery. It is particularly useful as an equipment option for field laboratories in areas with limited access to resources for water quality monitoring.

This paper describes a method for building an adaptable, low-cost and transportable incubator for microbial testing of drinking water. Our design is based on widely available materials and can operate under a range of field conditions, while still offering the advantages of higher-end laboratory-based models.

Incubators are essential for a range of culture-based microbial methods, such as membrane filtration followed by cultivation for assessing drinking water ...

BtM, a Low-cost Open-source Datalogger to Estimate the Water Content of Nonvascular Cryptogams

Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the carbon and nitrogen cycles in many ecosystems. Being poikilohydric organisms, they do not actively control their internal water content and need a humid environment to activate their metabolism. Therefore, studying water relationships of nonvascular cryptogams is crucial to understand both their diversity patterns and their functions in the ecosystems. We present the BtM datalogger, a low-cost open-source platform for the study of the water content of nonvascular cryptogams. The datalogger is designed to measure ambient temperature, humidity, and conductance from up to eight samples simultaneously. We provide a design for a printed circuit board (PCB), a detailed protocol to assemble the components, and the required source code. All this makes the assembly of the BtM datalogger accessible to any research group, even to those without previous specialized knowledge. Therefore, the design presented here has the potential to help popularize the use of this type of device among ecologists and field biologists.

We present a simple and cost-effective method to build an open-source datalogger that measures the conductance of nonvascular cryptogams together with the environmental temperature and humidity. We describe the hardware design of the datalogger and provide step-by-step assembly instructions, the list of required open-source logging software, the code to run the datalogger, and a calibration protocol.

Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the ...

Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and shape of activated sludge flocs can indicate the conditions at the microscale, and also directly affect how well the sludge settles in a clarifier.
Particle size and shape are both misleadingly &#39;simple&#39; measurements. Many subtle issues, often unaddressed in informal protocols, can arise when sampling, imaging, and analyzing particles. Sampling methods may be biased or not provide enough statistical power. The samples themselves may be poorly preserved or undergo alteration during immobilization. Images may not be of sufficient quality; overlapping particles, depth of field, magnification level, and various noise can all produce poor results. Poorly specified analysis can introduce bias, such as that produced by manual image thresholding and segmentation.
Affordability and throughput are desirable alongside reproducibility. An affordable, high throughput method can enable more frequent particle measurement, producing many images containing thousands of particles. A method that uses inexpensive reagents, a common dissecting microscope, and freely-available open source analysis software allows repeatable, accessible, reproducible, and partially-automated experimental results. Further, the product of such a method can be well-formatted, well-defined, and easily understood by data analysis software, easing both within-lab analyses and data sharing between labs.
We present a protocol that details the steps needed to produce such a product, including: sampling, sample preparation and immobilization in agar, digital image acquisition, digital image analysis, and examples of experiment-specific figure generation from the analysis results. We have also included an open-source data analysis pipeline to support this protocol.

The size and shape of particles in activated sludge are important parameters that are measured using varying methods. Inaccuracies arise from non-representative sampling, suboptimal images, and subjective analysis parameters. To minimize these errors and ease measurement, we present a protocol specifying every step, including an open source software pipeline.

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and ...

Using Caenorhabditis elegans for Studying Trans- and Multi-Generational Effects of Toxicants

Information about toxicities of chemicals are essential in their application and waste management. For chemicals at low concentrations, the long-term effects are very important in judging their consequences in the environment and on human health. In demonstrating long-term influences, effects of chemicals over generations in recent studies provide new insight. Here, we describe protocols for studying effects of chemicals over multiple generations using free-living nematode Caenorhabditis elegans. Two aspects are presented: (1) trans-generational (TG) and (2) multi-generational effect studies, the latter of which is separated to multi-generational exposure (MGE) and multi-generational residual (MGR) effect studies. The TG effect study is robust with a simple purpose to determine whether chemical exposure to parents can result in any residual consequences on offspring. After the effects are measured on parents, sodium hypochlorite solutions are used to kill the parents and keep the offspring so as to facilitate effect measurement on the offspring. The TG effect study is used to determine whether the offspring are affected when their parent is exposed to the pollutants. The MGE and MGR effect study is systematical used to determine whether continuous generational exposure can result in adaptive responses in offspring over generations. Careful pick-up and transfer are used to distinguish generations to facilitate effect measurement on each generation. We also combined protocols to measure locomotion behavior, reproduction, lifespan, biochemical and gene expression changes. Some example experiments are also presented to illustrate the trans- and multi-generational effect studies.

Using Caenorhabditis elegans for Studying Trans- and Multi-Generational Effects of Toxicants

Trans- and multi-generational effects of persistent chemicals are essential in judging their long-term consequences in the environment and on the human health. We provide novel detailed methods for studying trans- and multi-generational effects using free-living nematode Caenorhabditis elegans.

Information about toxicities of chemicals are essential in their application and waste management. For chemicals at low concentrations, the long-term ...

Manufacturing Simple and Inexpensive Soil Surface Temperature and Gravimetric Water Content Sensors

Quantifying temperature and moisture at the soil surface is essential for understanding how soil surface biota respond to changes in the environment. However, at the soil surface these variables are highly dynamic and standard sensors do not explicitly measure temperature or moisture in the upper few millimeters of the soil profile. This paper describes methods for manufacturing simple, inexpensive sensors that simultaneously measure the temperature and moisture of the upper 5 mm of the soil surface. In addition to sensor construction, steps for quality control, as well as for calibration for various substrates, are explained. The sensors incorporate a Type E thermocouple to measure temperature and assess soil moisture by measuring the resistance between two gold-plated metal probes at the end of the sensor at a depth of 5 mm. The methods presented here can be altered to customize probes for different depths or substrates. These sensors have been effective in a variety of environments and have endured months of heavy rains in tropical forests as well as intense solar radiation in deserts of the southwestern U.S. Results demonstrate the effectiveness of these sensors for evaluating warming, drying, and freezing of the soil surface in a global change experiment.

Accurately measuring temperature and water content of the upper 5 mm of the soil surface can improve our understanding of environmental controls on biological, chemical, and physical processes. Here we describe a protocol for manufacturing, calibrating, and conducting measurements with soil surface temperature and moisture sensors.

Quantifying temperature and moisture at the soil surface is essential for understanding how soil surface biota respond to changes in the environment. ...