We would like to acknowledge support received from Georgia Rhodes and Stuart Copeland in the inception of this project-their encouragement and mentorship was essential to our success. We would also like to highlight the utility of&#160;https://p5js.org/reference/ as a resource in learning to code in JavaScript. This material is based upon work supported in part by the National Science Foundation under EPSCoR Cooperative Agreement #OIA-1655221 and their Vis-a-Thon program&#160;and by the Rhode Island Sea Grant [NA23OAR4170086].

1. Playing the existing visualizations
<ol>
	<li>Download coding and visualization software (see Table of Materials).
	<ol>
		<li>Download the data and code. This article uses &#39;degrees of uncertainty&#39; with data from Marcks et al.4 and Cartagena-Sierra et al.5 on the age model from Starr et al.9. 
		NOTE: The &#39;degrees of uncertainty&#39; contains five coding files, Supplementary Coding File 1, Supplementary Coding File 2, Supplementary Coding File 3, Supplementary Coding File 4, and Supplementary Coding File 5, with contents pertaining to each time period of visualization (MPT 1, MPT 2, MPT 3, MPT 4, and Future, respectively). Each of these contains coding libraries10 used for visualizations as well as &#39;Script&#39; folders containing downloaded data in .csv format, code used to generate visuals &#39;particle.js&#39;, and an index file &#39;index.html&#39; which links all relevant data and code together.</li>
	</ol>
	</li>
	<li>Open the code editing software from the &#39;degrees of uncertainty&#39;.</li>
	<li>Drag a file (MPT 1, MPT 2, MPT 3, or MPT 4) into the code editor to visualize it.
	<ol>
		<li>The files appear in the EXPLORER menu on the left-hand side of the window. Check the procedure for visualizing data from the &#39;Future&#39; folder in step 1.7.</li>
	</ol>
	</li>
	<li>In the EXPLORER menu, click on the folder (MPT 1, MPT 2, MPT 3, or MPT 4) to reveal a drop-down menu, click on script, and then click on index.html. 
	NOTE: The code appears on the right-hand side of the window.</li>
	<li>Left-click the portion of the window with code for &#39;index.html&#39; and select open with live server from the menu. 
	NOTE: An internet browser window opens and begins playing the visualization.</li>
	<li>Closing and reopening the code editor may be necessary between visualizations when loading a visual from a different subset of time. Repeat steps 1.4-1.6 for each subset of time.</li>
	<li>To view the visualization based on future projections, open the &#39;Future&#39; folder on the computer and drag either the &#39;Accumulation&#39; or &#39;Transition&#39; folder into the code editor. The difference between animations is described in the results section.</li>
	<li>Select the folder name in the EXPLORER window and click on index.html. Left-click the portion of the window with code for &#39;index.html&#39; and select open with live server from the menu. 
	&#8203;NOTE: An internet browser window opens and begins playing the visualization, which can be saved locally on a computer by screen recording.</li>
</ol>
2. Editing the visualizations
NOTE: To edit the visualizations, follow steps 1.1-1.4 above, as necessary, to load the relevant data.
<ol>
	<li>Select the folder of interest in the EXPLORER window of the code editor and open the main script file by clicking on sketch.js. 
	NOTE: The &#39;sketch.js&#39; file in the MPT 1 (Supplementary Coding File 1) contains the most detailed annotations; thus, this file may be the most useful for familiarizing the code.
	<ol>
		<li>The code appears on the right-hand side of the code editor window. Perform any edits to visualization parameters within this code. Look for code annotations with detailed descriptions of the code and its function following double slashes &#34;//&#34; and further identified by green text (Supplementary Figure 1).</li>
		<li>Define the variables that will be linked to data or used to customize visual parameters (Supplementary Figure 1).</li>
		<li>Load the data into the workspace (Supplementary Figure 2).</li>
		<li>Define the visual parameters of the canvas. Use a &#39;for&#39; loop to link data to specific characteristics; here, size is linked to nitrogen isotopic value &#39;d15N&#39; (Supplementary Figure 3).</li>
		<li>Use a for loop to define a tail length for each orb. The tail refers to the length of time that the orbs remain on screen after appearing, creating an accumulation of color as the visual progresses (Supplementary Figure 4). 
		NOTE: Here, the tail length is scaled to the accumulation rate of alkenones&#39; c37.</li>
		<li>Finally, draw the animation, applying a Perlin Noise algorithm11 to define the shape of the visuals (Supplementary Figure 5). 
		&#8203;NOTE: Here, a circle is used as the base shape with noise applied to the points along the circumference of the circle. These will &#39;wiggle&#39; the boundary of the circle, yielding an organic orb-like shape that deviates from a circle in an amount defined by the &#39;wiggle&#39; command.</li>
		<li>Edit the code as necessary using annotations to aid the alterations.</li>
	</ol>
	</li>
</ol>
3. Saving the edits
<ol>
	<li>Save the edits by pressing the command and S keys at the same time.</li>
	<li>View updated visuals by navigating to the &#39;index.html&#39; file in the EXPLORER window, left-clicking, and selecting open with live server from the menu. 
	NOTE: An internet browser window opens and begins playing the visualization, which can be saved locally on the computer by screen recording.</li>
</ol>

<ol>
	<li>Anadol, R. e. f. i. k. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Refik Anadol. , (2023).</li><li>Lieberman, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Paint with your Feet. , (2011).</li><li>Moore, F. C., Obradovich, N., Lehner, F., Baylis, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapidly+declining+remarkability+of+temperature+anomalies+may+obscure+public+perception+of+climate+change.">Rapidly declining remarkability of temperature anomalies may obscure public perception of climate change.</a> Proceedings of the National Academy of Sciences. 116 (11), 4905-4910 (2019).</li><li>Marcks, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#948;15N+in+planktonic+foraminifera+species+G.+bulloides+and+G.+inflata+from+IODP+Site+361-U1475.+[Dataset].">&#948;15N in planktonic foraminifera species G. bulloides and G. inflata from IODP Site 361-U1475. [Dataset].</a> PANGAEA. , (2022).</li><li>Cartagena-Sierra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Latitudinal+migrations+of+the+subtropical+front+at+the+Agulhas+plateau+through+the+mid-Pleistocene+transition.">Latitudinal migrations of the subtropical front at the Agulhas plateau through the mid-Pleistocene transition.</a> Paleoceanography and Paleoclimatology. 36 (7), e2020PA004084 (2021).</li><li>Ford, H. L., Chalk, T. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mid-Pleistocene+enigma.">The mid-Pleistocene enigma.</a> Oceanography. 33 (2), 101-103 (2020).</li><li>. U.S. Climate Resilience Toolkit Climate Explorer Available from: <a target="_blank" href="https://crt-climate-explorer.nemac.org/">https://crt-climate-explorer.nemac.org/</a> (2021)</li><li>Stocker, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> IPCC: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. , 1535 (2013).</li><li>Starr, A., 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=Antarctic+icebergs+reorganize+ocean+circulation+during+Pleistocene+glacials.">Antarctic icebergs reorganize ocean circulation during Pleistocene glacials.</a> Nature. 589 (7841), 236-241 (2021).</li><li>Li, Q., McCarthy, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> P5.js. , (2023).</li><li>Perlin, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improving+noise.">Improving noise.</a> Proceedings of the 29th Annual Conference on Computer Graphics and Interactive Techniques. , 681-682 (2002).</li><li>Lisiecki, L. E., Raymo, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Pliocene-Pleistocene+stack+of+57+globally+distributed+benthic+&#948;18O+records.">A Pliocene-Pleistocene stack of 57 globally distributed benthic &#948;18O records.</a> Paleoceanography. 20 (1), PA1003 (2005).</li><li>Robinson, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insights+from+fossil-bound+nitrogen+isotopes+in+diatoms,+foraminifera,+and+corals.">Insights from fossil-bound nitrogen isotopes in diatoms, foraminifera, and corals.</a> Annual Review of Marine Science. 15, 407-430 (2023).</li></ol>

The authors acknowledge that no known conflicts of interest exist at this time

This work highlights the utility of generative art for the purpose of science communication. The workflow can be used to translate existing data to elements within an animation. While the animation outputs from this work are unique in that each time the code is run a different version of the animation is created, the visual elements are scaled to geochemical and climate model data; thus, elements such as color, speed, and size remain constant, so long as the input data remains the same. This also allows for the direct co...

Generative art and the methods employed here allow for the direct translation of quantitative data into animations while preserving the integrity of the data. Artists use generative art to explore perceptions of space and time1,2, but generative art is not yet commonly used with spatial or temporal scientific data. The work presented here provides a simple framework for using generative visual products to showcase climate data. These products can be widely applied, whether used to create in-person exhibits or as a visual aid for a presentation or online publication.
Using geochemical measurements or estimates to scale elements such as color, shape, size, and speed provides a means of visually conveying rates and magnitudes of change without requiring the viewer to read a paper, interpret a graph, or look through a data table. Alternatively, the randomization of selected variables is used to convey a lack of data or uncertainty, as in the case of future projections. The juxtaposition of geologic past and future is perhaps integral to the effectiveness of these products as science communication tools. Recent experiences often serve as the baseline of comparison for modern climate change, making it difficult to grasp the magnitude of anthropogenic climate change3.
Geochemical measurements visualized in this paper span the mid-Pleistocene transition (MPT; 1.2 million to 600,000 years ago), recording changes near the northern boundary of the Southern Ocean from International Ocean Discovery Program Site U14754,5. The MPT data is presented in four animations, which highlight changes in ocean conditions as the planet cools and glacial and interglacial variability is amplified6. This provides a geologic baseline revealing the natural rhythm of Earth&#39;s climate, emphasizing a long-term cooling trend that starkly contrasts future climate projections. Future temperature estimates are average values of the results of 20 climate models under the forcings of Representative Carbon Pathway 8.5 (RCP 8.5; scenario with a radiative forcing of 8.5 W/m2 in the year 2100) for the location New York, NY7. RCP 8.5 represents a worst-case scenario of sustained emissions resulting in a 3.7 &#176;C increase in average global temperature by 21008. Thus, this article demonstrates a means of comparing future projections with geologic data to compare rates of climate change and climate variability.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Easel</td>
			<td>Uline</td>
			<td>H-1450SIL</td>
			<td>Telescoping easel to hold foam core board</td>
		</tr>
		<tr>
			<td>Foam Core Poster Board</td>
			<td>Royal Brites</td>
			<td>#753064</td>
			<td>Foam core board used as a canvas for projection</td>
		</tr>
		<tr>
			<td>Live Server</td>
			<td>Microsoft; Publisher: Ritwick Dey</td>
			<td>Version 5.7.9</td>
			<td>Software extension for Visual Studio Code which allows for viewing of animations in a browser window. Downloaded at: https://marketplace.visualstudio.com/items?itemName=ritwickdey.LiveServer</td>
		</tr>
		<tr>
			<td>Throw Projector</td>
			<td>Optoma</td>
			<td>796435814076</td>
			<td>Any model throw projector which will work for projection surface/distance desired&#160;</td>
		</tr>
		<tr>
			<td>Visual Studio Code</td>
			<td>Microsoft</td>
			<td>Version 1.74 for MAC OS</td>
			<td>Software for code editing and execusion. Downloaded at : https://code.visualstudio.com/</td>
		</tr>
	</tbody>
</table>

using generative art to convey past and future climate transitions

The ability to understand modern day climate relies on a foundational understanding of past climate variability and the ways in which the planet is stabilized by interconnected feedbacks. This article presents a unique method for translating records of past climate transitions preserved in deep-sea sediments to broad audiences through an immersive visualization. This visualization is a multimedia installation that incorporates geochemical records of glacial and interglacial transitions and model predictions for future anthropogenic warming to create an immersive experience for viewers, inviting them to engage with and reflect on the subtle, nuanced differences between subsets of Earth&#39;s history. This work showcases five intervals of time, beginning with the inception of modern glacial-interglacial cyclicity (~one million years ago), comparing past climate with model results for projected future anthropogenic warming (until 2099). The installation consists of several experimental projections, one for each subset of time, displayed on different surfaces in a room. As viewers move through the space, the projections slowly cycle through different climatic transitions, using animation methods like speed, color, layering, and repetition, all generated through site-specific data to convey the planet&#39;s unique behavior as it relates to global climate. This work provides a framework for unique scientific data visualization, with generative animations created using a Perlin Noise algorithm at the center of the installation. Research variables, like sea surface temperature, nutrient dynamics, and the rate of climate change, impact formal outcomes like color, scale, and animation speed, which are all easy to manipulate and connect to specific data. This approach also allows the possibility of publishing data online and provides a mechanism for scaling visual parameters to a wide variety of quantitative and qualitative data.

This work produces six visualizations corresponding to five unique intervals of geologic time, with visual aspects scaled to quantitative data either measured on deep-sea sediment (Figure 1, Figure 2, Figure 3, Figure 4, Video 1, Video 2, Video 3, and Video 4) or modeled from the Intergovernmental Panel on Climate Change&#39;s (IPCC) RC...

Watch this Scientific Journal Video about Using Generative Art to Convey Past and Future Climate Transitions at JoVE.com

Using Generative Art to Convey Past and Future Climate Transitions

Here, a protocol is presented to visualize climate data as generative art.

The ability to understand modern day climate relies on a foundational understanding of past climate variability and the ways in which the planet is ...

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787 Views.  University of Rhode Island. Here, a protocol is presented to visualize climate data as generative art. 

Video: Using Generative Art to Convey Past and Future Climate Transitions

Integrating Remote Sensing with Species Distribution Models; Mapping Tamarisk Invasions Using the Software for Assisted Habitat Modeling (SAHM)

Early detection of invasive plant species is vital for the management of natural resources and protection of ecosystem processes. The use of satellite remote sensing for mapping the distribution of invasive plants is becoming more common, however conventional imaging software and classification methods have been shown to be unreliable. In this study, we test and evaluate the use of five species distribution model techniques fit with satellite remote sensing data to map invasive tamarisk (Tamarix spp.) along the Arkansas River in Southeastern Colorado. The models tested included boosted regression trees (BRT), Random Forest (RF), multivariate adaptive regression splines (MARS), generalized linear model (GLM), and Maxent. These analyses were conducted using a newly developed software package called the Software for Assisted Habitat Modeling (SAHM). All models were trained with 499 presence points, 10,000 pseudo-absence points, and predictor variables acquired from the Landsat 5 Thematic Mapper (TM) sensor over an eight-month period to distinguish tamarisk from native riparian vegetation using detection of phenological differences. From the Landsat scenes, we used individual bands and calculated Normalized Difference Vegetation Index (NDVI), Soil-Adjusted Vegetation Index (SAVI), and tasseled capped transformations. All five models identified current tamarisk distribution on the landscape successfully based on threshold independent and threshold dependent evaluation metrics with independent location data. To account for model specific differences, we produced an ensemble of all five models with map output highlighting areas of agreement and areas of uncertainty. Our results demonstrate the usefulness of species distribution models in analyzing remotely sensed data and the utility of ensemble mapping, and showcase the capability of SAHM in pre-processing and executing multiple complex models.

Integrating Remote Sensing with Species Distribution Models; Mapping Tamarisk Invasions Using the Software for Assisted Habitat Modeling SAHM

We demonstrate the utility of remotely sensed data and the newly developed Software for Assisted Habitat Modeling (SAHM) in predicting invasive species occurrence on the landscape. An ensemble of predictive models produced highly accurate maps of tamarisk (Tamarix spp.) invasion in Southeastern Colorado, USA when assessed with subsequent field validations.

Early detection of invasive plant species is vital for the management of natural resources and protection of ecosystem processes. The use of satellite ...

Implementation of Portable Emissions Measurement Systems (PEMS) for the Real-driving Emissions (RDE) Regulation in Europe

Vehicles are tested in controlled and relatively narrow laboratory conditions to determine their official emission values and reference fuel consumption. However, on the road, ambient and driving conditions can vary over a wide range, sometimes causing emissions to be higher than those measured in the laboratory. For this reason, the European Commission has developed a complementary Real-Driving Emissions (RDE) test procedure using the Portable Emissions Measurement Systems (PEMS) to verify gaseous pollutant and particle number emissions during a wide range of normal operating conditions on the road. This paper presents the newly-adopted RDE test procedure, differentiating six steps: 1) vehicle selection, 2) vehicle preparation, 3) trip design, 4) trip execution, 5) trip verification, and 6) calculation of emissions. Of these steps, vehicle preparation and trip execution are described in greater detail. Examples of trip verification and the calculations of emissions are given.

Implementation of Portable Emissions Measurement Systems PEMS for the Real-driving Emissions RDE Regulation in Europe

The European Commission has developed a Real-Driving Emissions (RDE) test procedure to verify pollutant emissions during real-world vehicle operation using the Portable Emissions Measurement Systems (PEMS). This paper presents the experimental procedures required by the newly-adopted RDE test.

Vehicles are tested in controlled and relatively narrow laboratory conditions to determine their official emission values and reference fuel consumption. ...

Using Pharmacological Manipulation and High-precision Radio Telemetry to Study the Spatial Cognition in Free-ranging Animals

An animal&#39;s ability to perceive and learn about its environment plays a key role in many behavioral processes, including navigation, migration, dispersal and foraging. However, the understanding of the role of cognition in the development of navigation strategies and the mechanisms underlying these strategies is limited by the methodological difficulties involved in monitoring, manipulating the cognition of, and tracking wild animals. This study describes a protocol for addressing the role of cognition in navigation that combines pharmacological manipulation of behavior with high-precision radio telemetry. The approach uses scopolamine, a muscarinic acetylcholine receptor antagonist, to manipulate cognitive spatial abilities. Treated animals are then monitored with high frequency and high spatial resolution via remote triangulation. This protocol was applied within a population of Eastern painted turtles (Chrysemys picta) that has inhabited seasonally ephemeral water sources for ~100 years, moving between far-off sources using precise (&#177; 3.5 m), complex (i.e., non-linear with high tortuosity that traverse multiple habitats), and predictable routes learned before 4 years of age. This study showed that the processes used by these turtles are consistent with spatial memory formation and recall. Together, these results are consistent with a role of spatial cognition in complex navigation and highlight the integration of ecological and pharmacological techniques in the study of cognition and navigation.

This paper describes a novel protocol that combines the pharmacological manipulation of memory and radio telemetry to document and quantify the role of cognition in navigation.

An animal&#39;s ability to perceive and learn about its environment plays a key role in many behavioral processes, including navigation, migration, ...

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition.
An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. 
This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.

The article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples.

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial ...

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.

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 ...

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, ...

Using Tg(Vtg1:mcherry) Zebrafish Embryos to Test the Estrogenic Effects of Endocrine Disrupting Compounds

There are many endocrine disrupting compounds (EDC) in the environment, especially estrogenic substances. The detection of these substances is difficult due to their chemical diversity; therefore, increasingly more effect-detecting methods are used, such as estrogenic effect-sensitive biomonitor/bioindicator organisms. These biomonitoring organisms include several fish models. This protocol covers the use of zebrafish Tg(vtg1: mCherry) transgenic line as a biomonitoring organism, including the propagation of fish and the treatment of embryos, with an emphasis on the detection, documentation, and evaluation of fluorescent signals induced by EDC. The goal of the work is the demonstration of the use of the Tg(vtg1: mCherry) transgenic line embryos to detect estrogenic effects. This work documents the use of transgenic zebrafish embryos Tg(vtg1: mCherry) for the detection of estrogenic effects by testing two estrogenic substances, &#945;- and &#946;-zearalenol. The described protocol is only a basis for designing assays; the test method can be varied according to the test endpoints and the samples. Moreover, it can be combined with other assay methods, thereby facilitating the future use of the transgenic line.

Using TgVtg1:mcherry Zebrafish Embryos to Test the Estrogenic Effects of Endocrine Disrupting Compounds

Present here is a detailed protocol for the use of zebrafish embryos Tg(vtg1: mCherry) for the detection of estrogenic effects. The protocol covers the propagation of the fish and treatment of embryos, and emphasizes the detection, documentation, and the evaluation of fluorescent signals induced by endocrine disrupting compounds (EDC).

There are many endocrine disrupting compounds (EDC) in the environment, especially estrogenic substances. The detection of these substances is difficult ...

In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems

Microbial behaviors, such as motility and chemotaxis (the ability of a cell to alter its movement in response to a chemical gradient), are widespread across the bacterial and archaeal domains. Chemotaxis can result in substantial resource acquisition advantages in heterogeneous environments. It also plays a crucial role in symbiotic interactions, disease, and global processes, such as biogeochemical cycling. However, current techniques restrict chemotaxis research to the laboratory and are not easily applicable in the field. Presented here is a step-by-step protocol for the deployment of the in situ chemotaxis assay (ISCA), a device that enables robust interrogation of microbial chemotaxis directly in the natural environment. The ISCA is a microfluidic device consisting of a 20 well array, in which chemicals of interest can be loaded. Once deployed in aqueous environments, chemicals diffuse out of the wells, creating concentration gradients that microbes sense and respond to by swimming into the wells via chemotaxis. The well contents can then be sampled and used to (1) quantify strength of the chemotactic responses to specific compounds through flow cytometry, (2) isolate and culture responsive microorganisms, and (3) characterize the identity and genomic potential of the responding populations through molecular techniques. The ISCA is a flexible platform that can be deployed in any system with an aqueous phase, including marine, freshwater, and soil environments.

Presented here is the protocol for an in situ chemotaxis assay, a recently developed microfluidic device that enables studies of microbial behavior directly in the environment.

Microbial behaviors, such as motility and chemotaxis (the ability of a cell to alter its movement in response to a chemical gradient), are widespread ...

Microplot Design and Plant and Soil Sample Preparation for 15Nitrogen Analysis

Many&#160;nitrogen fertilizer studies evaluate the overall effect of a treatment on end-of-season measurements such as grain yield or cumulative N losses. A stable isotope approach is necessary to follow and quantify the fate of fertilizer derived N (FDN) through the soil-crop system. The purpose of this paper is to describe a small-plot research&#160;design utilizing non-confined 15N enriched microplots for multiple soil and plant sampling events over two growing seasons and provide sample collection, handling, and processing protocols for total 15N analysis. The methods were demonstrated using a replicated study from south-central Minnesota planted to corn (Zea mays L.). Each treatment consisted of six corn rows (76 cm row-spacing) 15.2 m long with a microplot (2.4 m by 3.8 m) embedded at one end. Fertilizer-grade urea was applied at 135 kg N&#8729;ha-1 at planting, while the microplot received urea enriched to 5 atom % 15N. Soil and plant samples were taken several times throughout the growing season, taking care to minimize cross-contamination by using separate tools and physically separating unenriched and enriched samples during all procedures. Soil and plant samples were dried, ground to pass through a 2 mm screen, and then ground to a flour-like consistency using a roller jar mill. Tracer studies require additional planning, sample processing time and manual labor, and incur higher costs for 15N enriched materials and sample analysis than traditional N studies. However, using the mass balance approach, tracer studies with multiple in-season sampling events allow the researcher to estimate FDN distribution through the soil-crop system and estimate unaccounted-for FDN from the system.

Microplot Design and Plant and Soil Sample Preparation for 15Nitrogen Analysis

A microplot design for 15N tracer research is described to accommodate multiple in-season plant and soil sampling events. Soil and plant sample collection and processing procedures, including grinding and weighing protocols, for 15N analysis are put forth.

Many&#160;nitrogen fertilizer studies evaluate the overall effect of a treatment on end-of-season measurements such as grain yield or cumulative N losses. ...

Using Changes in Leaf Transmission to Investigate Chloroplast Movement in Arabidopsis thaliana

Chloroplast movement in leaves has been shown to help minimize photoinhibition and increase growth under certain conditions. Much can be learned about chloroplast movement by studying the chloroplast positioning in leaves using e.g., confocal fluorescence microscopy, but access to this type of microscopy is limited. This protocol describes a method that uses the changes in leaf transmission as a proxy for chloroplast movement. If chloroplasts are spread out in order to maximize light interception, the transmission will be low. If chloroplasts move towards the anticlinal cell walls to avoid light, the transmission will be higher. This protocol describes how to use a straightforward, home-built instrument to expose leaves to different blue light intensities and quantify the dynamic changes in leaf transmission. This approach allows researchers to quantitatively describe chloroplast movement in different species and mutants, study the effects of chemicals and environmental factors on it, or screen for novel mutants e.g., to identify missing components in the process that leads from light perception to the movement of chloroplasts.

Using Changes in Leaf Transmission to Investigate Chloroplast Movement in Arabidopsis thaliana

Many plant species change the positioning of chloroplasts to optimize light absorption. This protocol describes how to use a straightforward, home-built instrument to investigate chloroplast movement in Arabidopsis thaliana leaves using changes in the transmission of light through a leaf as a proxy.

Chloroplast movement in leaves has been shown to help minimize photoinhibition and increase growth under certain conditions. Much can be learned about ...