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><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&amp;nbsp;</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 ...

using-generative-art-to-convey-past-and-future-climate-transitions

Research

JoVE Journal

Environment

868 Views.  University of Rhode Island. Het kan een uitdaging zijn om klimaatgegevens over te brengen, vooral wanneer de tijdschalen veel groter zijn dan waar mensen gewoonlijk aan denken. Met dit protocol kunnen gebruikers generatieve animaties maken met visuals die zijn geschaald naar gegevens. Met deze procedure kunnen de gegevens worden omgezet in animaties die informatie overbrengen zonder afhankelijk te zijn van diagrammen of grafieken.Het is zeer aanpasbaar in termen van gebruikte gegevens en de weergegeven visuele as...

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

Visualizing Visual Adaptation

Many techniques have been developed to visualize how an image would appear to an individual with a different visual sensitivity: e.g., because of optical or age differences, or a color deficiency or disease. This protocol describes a technique for incorporating sensory adaptation into the simulations. The protocol is illustrated with the example of color vision, but is generally applicable to any form of visual adaptation. The protocol uses a simple model of human color vision based on standard and plausible assumptions about the retinal and cortical mechanisms encoding color and how these adjust their sensitivity to both the average color and range of color in the prevailing stimulus. The gains of the mechanisms are adapted so that their mean response under one context is equated for a different context. The simulations help reveal the theoretical limits of adaptation and generate &#34;adapted images&#34; that are optimally matched to a specific environment or observer. They also provide a common metric for exploring the effects of adaptation within different observers or different environments. Characterizing visual perception and performance with these images provides a novel tool for studying the functions and consequences of long-term adaptation in vision or other sensory systems.

This article describes a novel method for simulating and studying adaptation in the visual system.

Many techniques have been developed to visualize how an image would appear to an individual with a different visual sensitivity: e.g., because of optical ...

Behavior

Using Tree-Rings to Reconstruct Fire History Information from Forested Areas

Annual tree-ring patterns are a source of ecological and environmental information including the history of fires in forested areas. Tree-ring based fire histories include three fundamental phases: field collection, laboratory methods (preparation and dating), and data analysis. Here we provide step-by-step instructions and issues to consider, including the process for selecting the study area, sampling sites, plus how and which fire-scarred trees to sample. In addition, we describe fire-scar sample preparation and dating which are done in the laboratory. Finally, we describe basic analysis and relevant results, including examples from studies that have reconstructed fire history patterns. These studies allow us to understand the historical fire frequency, changes in those frequencies related to anthropogenic factors, and analyzes of how climate influences fire occurrence over time. The description of these methods and techniques should provide a greater understanding of fire history studies that will benefit researchers, educators, technicians, and students interested in this field. These detailed methods will allow new researchers to this field, a resource to start their own work and achieve greater success. This resource will provide a greater integration of tree-ring aspects within other studies and lead to a better understanding of natural processes with forested ecosystems.

This work explains the most appropriate techniques and methods for conducting a fire history study from beginning site selection to final analysis of fire-climate relationship.

Annual tree-ring patterns are a source of ecological and environmental information including the history of fires in forested areas. Tree-ring based fire ...

How to Extract Climate Variability from Tree-Rings

Tree rings have been used to reconstruct climatological variables in many locations around the world. Moreover, tree-rings can provide valuable insights into climatic variability of the last few centuries and, in some areas, several millennia. Despite the important development, that dendrochronology has had in recent decades to study the dendroclimatic potential of a large number of species present in different ecosystems, much remains to be done and explored. In addition to this, in the last few years more people (students, teachers and researchers) around the world are interested in implementing this science to extend the timeline of climate information backwards and understand how climate has changed on scales of decades, centuries or millennia. Therefore, the objective of this work is to describe the general aspects and basic steps needed to conduct a tree-ring climate reconstruction, from site selection and field sampling to laboratory methods and data analysis. In this method's video and manuscript, the general basis in tree-ring climatic reconstructions is explained so newcomers and students can use it as an available guide into this field of research.

Tree-ring climate reconstructions can be helpful to better understand past climate variability beyond instrumental records. This protocol shows how to reconstruct past climate using tree rings and meteorological instrumental records.

Tree rings have been used to reconstruct climatological variables in many locations around the world. Moreover, tree-rings can provide valuable insights ...

Exploring Long-Term Shifts in Phytoplankton by Conversion of Microscopic Images

Visualizing Oceanographic Data to Depict Long-term Changes in Phytoplankton

Oceanographic time series provide&#160;an important perspective on environmental processes in ecosystems. The Narragansett Bay Long-Term Plankton Time Series (NBPTS) in Narragansett Bay, Rhode Island, USA, represents one of the longest plankton time series (1959-present) of its kind in the world and presents a unique opportunity to visualize long-term change within an aquatic ecosystem. Phytoplankton represent&#160;the base of the food web in most marine systems, including Narragansett Bay. Therefore, communicating their importance to the 2.4 billion people who live within the coastal ocean is critical. We developed a protocol with the goal of visualizing the diversity and magnitude of phytoplankton by utilizing Adobe Illustrator to convert microscopic images of phytoplankton collected from the NBPTS into vector graphics that could be conformed into repetitive visual patterns through time. Numerically abundant taxa or those that posed economic and health threats, such as the harmful algal bloom taxa, Pseudo-nitzschia spp., were selected for image conversion. Patterns of various phytoplankton images were then created based on their relative abundance for select decades of data collected (1970s, 1990s, and 2010s). Decadal patterns of phytoplankton biomass informed the outline of each decade while a background color gradient from blue to red was used to reveal a long-term temperature increase observed in Narragansett Bay. Finally, large, 96-inch by 34-inch panels were printed with repeating phytoplankton patterns to illustrate potential changes in phytoplankton abundance over time. This project enables visualization of literal shifts in phytoplankton biomass, that are typically invisible to the naked eye while leveraging real-time series data (e.g., phytoplankton biomass and abundance) within the art piece itself. It represents an approach that can be utilized for many other plankton time series for data visualization, communication, education, and outreach efforts.

Author Spotlight: Unveiling Plankton Response to Climate Change Through Time-Series Data and Artistic Expression 

Here, we present a protocol for converting phytoplankton microscopic images into vector graphics and repetitive patterns to enable visualization of shifts in phytoplankton taxa and biomass over 60 years. This protocol represents an approach that can be utilized for other plankton time series and datasets globally.

Oceanographic time series provide&#160;an important perspective on environmental processes in ecosystems. The Narragansett Bay Long-Term Plankton Time ...

Digital Leaf Physiognomy for Paleoclimate and Paleoecological Reconstruction

Reconstructing Terrestrial Paleoclimate and Paleoecology with Fossil Leaves Using Digital Leaf Physiognomy and Leaf Mass Per Area

Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants&#39; leaves. These relationships, particularly in woody non-monocotyledonous angiosperms, have been used to develop leaf-based proxies for paleoclimate and paleoecology that have been applied to reconstruct ancient terrestrial ecosystems for the last ~120 million years of Earth&#39;s history. Additionally, given that these relationships have been documented in living plants, they are important for understanding aspects of plant evolution and how plants respond to climatic and environmental changes. To conduct these types of analyses on modern and fossil plants, leaf physiognomy must be measured accurately using a reproducible methodology. This protocol describes a computer-based method for measuring and analyzing a variety of leaf physiognomic variables in modern and fossil leaves. This method allows for the measurement of leaf physiognomic traits, in particular variables related to leaf serrations, leaf area, leaf dissection, and linearity that are used in the digital leaf physiognomy proxy for reconstructing paleoclimate, as well as petiole width and leaf area, which are used for reconstructing leaf mass per area, a paleoecological proxy. Because this digital leaf trait measurement method can be applied to fossil and living plants, it is not limited to applications related to reconstructing paleoclimate and paleoecology. It can also be used to explore leaf traits that may be informative for understanding the function of leaf morphology, leaf development, phylogenetic relationships of leaf traits, and plant evolution.

Author Spotlight: Leaf Trait Analysis for Climate and Ecology Reconstruction in Modern and Ancient Plant Communities

The protocol presented shows digital measurement and analysis of continuous leaf physiognomic traits on fossil leaves to reconstruct paleoclimate and paleoecology using the digital leaf physiognomy and leaf mass per area reconstruction methods.

Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants&#39; leaves. These relationships, particularly in woody ...

Generation of Dynamical Environmental Conditions using a High-Throughput Microfluidic Device

Mimicking in vivo environmental conditions is crucial for in vitro studies on complex life machinery. However, current techniques targeting live cells and organs are either highly expensive, like robotics, or lack nanoliter volume and millisecond time accuracy in liquid manipulation. We herein present the design and fabrication of a microfluidic system, which consists of 1,500 culture units, an array of enhanced peristaltic pumps and an on-site mixing modulus. To demonstrate the capacities of the microfluidic device, neural stem cell (NSC) spheres are maintained in the proposed system. We observed that when the NSC sphere is exposed to CXCL in day 1 and EGF in day 2, the round-shaped conformation is well maintained. Variation in the input order of 6 drugs causes morphological changes to the NSC sphere and the expression level representative marker for NSC stemness (i.e., Hes5 and Dcx). These results indicate that dynamic and complex environmental conditions have great effects on NSC differentiation and self-renewal, and the proposed microfluidic device is a suitable platform for high throughput studies on the complex life machinery.

We present a microfluidic system for high throughput studies on complex life machinery, which consists of 1500 culture units, an array of enhanced peristaltic pumps and an on-site mixing modulus. The microfluidic chip allows for the analysis of the highly complex and dynamic micro-environmental conditions in vivo.

Mimicking in vivo environmental conditions is crucial for in vitro studies on complex life machinery. However, current techniques targeting live cells and ...

Bioengineering

Climate Change

The certainty of climate change remains a public controversy despite the consensus among approximately 97% of active climate researchers, who not only agree that the Earth&#8217;s climate is changing but also state that this change is intensified by human activity, predominantly carbon emissions 1. The disconnect between the public and the experts is partly due to poor understanding of the mechanisms involved in climate change as well as the differences among essential concepts such as weather and climate.
<h4>Climate versus Weather</h4>
Localized atmospheric conditions in a region over a short period of time, such as temperature and precipitation, are described as the weather. Climate involves these same conditions, however when measured over extended periods of time. Therefore, when scientists talk about the global climate, they refer to the statistical measures of climate data collected across the entire Earth. One prominent global climate measure is the global average temperature, which is the average of the temperatures recorded across the planet.
<h4>Monitoring Climate Change</h4>
Scientists study changes to the global climate over time and much of the research in climate change is based on the physical sciences, such as meteorology, geography, and oceanography. Further, computer scientists model the predicted effects of events such as polar ice melting causing sea level rise and increasing temperatures. These studies are imperative for biological research because climate change affects a myriad of species that have varied abilities to tolerate different climates.
A major component of climate change is global warming, defined as an increase in global average temperature of the atmosphere. Climate researchers recognize that increases in greenhouse gases raise global average temperatures. This is because greenhouse gases absorb infrared radiation transmitted from the sun and re-emit it as heat into the atmosphere. Subsequently, this heat is distributed throughout the different layers of the atmosphere and Earth&#8217;s surface. While heat radiates in all directions from greenhouse gas molecules, the surface of the Earth absorbs some of the heat that had radiated downward, which leads to increased surface temperatures and trapping of the heat energy in the lower atmosphere. This trapping of heat at the Earth&#8217;s surface due to the atmosphere is called the greenhouse effect.
Four major gases contribute to the greenhouse effect on Earth: water vapor, CO2, methane, and ozone. However, a particularly important greenhouse gas that plays a significant role in global warming and climate change is carbon dioxide (CO2). While CO2 has always been found in the Earth&#8217;s atmosphere, human-related activities such as fossil-fuel burning are increasing its abundance significantly. In the past 800,000 years, CO2 levels fluctuated without human-intervention between 180 parts per million (ppm) to 270 ppm in the atmosphere. In 2016 the concentration rose above 400ppm, which is staggeringly high considering historical fluctuations 2.
<h4>Predicting the Future</h4>
A prominent consequence of climate change is the sea level rise. As the climate warms, glacial ice melts due to a phenomenon known as the albedo effect. Albedo is a measure of reflected solar radiation as a proportion of total solar radiation received and ranges from 0 to 1. Albedo value depends on snow quality; dirtier or melted slow has a low albedo, whereas fresh and white snow has a high albedo. Antarctic snow generally has an albedo of around 0.8. As the temperature warms and the snow begins to melt, the albedo value gets lower, which means the snow reflects less of the radiation as heat and melts more, resulting in a positive feedback loop. Positive feedback loops occur when a perturbation to a system increases the magnitude of the response to the perturbation. So, the more the snow/ice melts due to warmer temperatures, the more it will melt due to its weakened ability to reflect solar radiation and the more heat is absorbs, causing it to melt further. This melting of ice causes the sea levels to increase. At present, the large ice sheets contain mass equivalent to almost 70 meter (m) of global sea-level rise, of which approximately 60 m mass equivalent is stored in Antarctic ice and nearly 7 m in Greenland 3. Smaller bodies of ice, such as glaciers and ice caps contain much less water, however, melting of these ice reservoirs dominated over larger ice sheets in the last decades because they respond quicker to a given climate forcing due to their smaller size 3.
Sea level rise is a critical threat to human wellbeing due to its potential in destroying properties near the coast, affecting coastal communities, and mediating ocean temperatures. The economic costs of sea level rise are vast; if the ocean level rises by just 1 meter, a sizable portion of Florida&#8217;s coastline would be under water, affecting 1.2 million people&#8217;s homes 4. Currently the Greenland ice sheet is thinning and if it were to be eliminated the sea levels would rise an estimated 5-7 meters, affecting millions more 3.
As the climate changes, it becomes important to track species distributions to see if these are also changing. Species are found across a geographical area known as their range. Scientists study the changes in the historical ranges of organisms, known as range shifts, in relation to a variety of environmental variables to predict whether species will be able to keep up with changes in temperature, precipitation and other weather patterns. Studying range shifts is important because if species cannot move to new areas and their current habitats become unsuitable, they will go extinct. For slow-growing organisms like plants and corals, it is nearly impossible to adapt to a quickly changing climate. Corals naturally inhabit clear, shallow reefs, and if they move deeper they will not be able to get the light they need for their photosynthetic symbiotic algae. As the water warms, symbiotic algae called zooxanthellae leave the corals which causes the corals to bleach and die. Surveys on the Australian Great Barrier Reef in 2016 show that up to 67% of corals have died in specific regions due to bleaching 5.
Human-induced carbon emissions contribute significantly to the levels of CO2 in the atmosphere, which in turn increases global temperature. In addition to this rise in global temperature, ocean acidification is also a direct result of increased CO2. The oceans absorb about a quarter of the CO2 in the atmosphere each year. When CO2 is absorbed by seawater, it is converted to carbonic acid (H2CO3), which in turn causes the seawater to become more acidic and reduce the availability of carbonate ions. Decreases in carbonate ions can hinder building and maintaining calcium carbonate structures of bivalves, sea urchins, and corals 6. Together with the rise of ocean temperatures, the acidification of the oceans can be detrimental for the aquatic ecosystems. 6
It is imperative to mediate the effects of climate change. Many scientists have begun researching what is currently called the Holocene Extinction, commonly known as the &#8220;Sixth Extinction&#8221; 7. There have been five major extinction events in the past, however, the rate of extinction in the past century has been 1000 times greater than expected &#8220;background extinction rates&#8221;. Habitat loss and climate change both play large roles in species extinction, making it important to maintain consideration of the environment in management decisions 7.
<h4>References</h4>
<ol class="references">
	<li>William R. L. Anderegg, James W. Prall, Jacob Harold, and Stephen H. Schneider. Expert credibility in climate change. PNAS. 2010, Vol. 107, 27 (12107-9).</li>
	<li>Richard A. Betts, Chris D. Jones, Jeff R. Knight, Ralph F. Keeling &#38; John J. Kennedy. El Ni&#241;o and a record CO2 rise. Nature Climate Change. 2016, Vol. 6, (806-10).</li>
	<li>Milne, Glenn. How the climate drives sea-level changes. Astronomy &#38; Geophysics. 2008, Vol. 49, 2 (2.24&#8211;2.28).</li>
	<li>Williams, S. Jeffress. Sea-Level Rise Implications for Coastal Regions. Journal of Coastal Research. 63 (184-96).</li>
	<li>Terry P Hughes, James T Kerry, Mariana &#193;lvarez-Noriega, Jorge G &#193;lvarez-Romero, Kristen D Anderson, Andrew H Baird, Russell C Babcock, Maria Beger, David R Bellwood, Ray Berkelmans, Tom C Bridge, Ian R Butler, Maria Byrne, Neal E Cantin, Steeve Comeau, Se. Global warming and recurrent mass bleaching of corals. Nature. 2017, Vol. 543, 7645 (373).</li>
	<li>F. Prada, E. Caroselli, S. Mengoli, L. Brizi, P. Fantazzini, B. Capaccioni, L. Pasquini, K. E. Fabricius, Z. Dubinsky, G. Falini &#38; S. Goffredo. Ocean warming and acidification synergistically increase coral mortality. Nature. 2017, 40842.</li>
	<li>Vredenburg, David B. Wake and Vance T. Are we in the midst of the sixth mass extinction? A view from the world of amphibians. PNAS. 2008, 1091-6490.</li>
</ol>

Climate Change: Ice Melt, Greenhouse Gas, and Species Range Activities - Concept

The certainty of climate change remains a public controversy despite the consensus among approximately 97% of active climate researchers, who not only ...

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Biology

Ecology

An Overview of bGDGT Biomarker Analysis for Paleoclimatology

Source: Laboratory of Jeff Salacup&#160;- University of Massachusetts Amherst
Throughout this series of videos, natural samples were extracted and purified in search of organic compounds, called biomarkers, that can relate information on climates and environments of the past. One of the samples analyzed was sediment. Sediments accumulate over geologic time in basins, depressions in the Earth into which sediment flows through the action of fluid (water or air), movement, and gravity. Two main types of basins exist, marine (oceans and seas) and lacustrine (lakes). As one might guess, very different types of life live in these settings, driven in large part by the difference in salinity between them. Over the last few decades, organic geochemists discovered a toolbox of biomarker proxies, or compounds that can be used to describe climate or environment, some of which work in marine environments and some of which work in lacustrine. We turn our attention here to the lacustrine realm and branched glycerol dialkyl glycerol tetraethers (Figure 1).
In this section we focus on analysis of terrestrial paleotemperature using branched glycerol dialkyl glycerol tetrathers (Figure 1; brGDGTs) and the MBT/CBT proxy. This proxy was initially described by Weijers et al.1&#160;and is based on the distribution of ring and branch structures in brGDGTs. They found that the cyclization of branched tetraethers (CBT) was directly related to soil pH.
CBT = -log ((Ib + IIb) / (I + II))
And that the methylation of branched tetraethers (MBT) was determined by mean annual air temperature (MAAT) and, to a lesser extent, soil pH.
MBT = (I + Ib + Ic) / (I + Ib + Ic) + (II + IIb + IIc) + (III + IIIb + IIIc)
Thus, taken together and calibrated, MBT/CBT relates the distribution of brGDGTs to both soil temperature and pH.
MBT = 0.122 + (0.187 x CBT) + (0.020 x MAAT)
Branched GDGTs are thought to be membrane spanning lipids and their production was initially attributed to anaerobic Acidobacteria bacteria living in soils and peat2-5, but subsequent work suggested they could also be produced in oxic and anoxic lake and marine water columns and sediments6-9. The hypothesis holds that Acidobacteria transform sites of methylation into cyclizations in response to lowering temperature in order to increase unsaturation (cyclization effectively removes two hydrogen atoms) and maintain membrane fluidity (by analogy, saturated fat (butter) is a solid a room temperature while unsaturated fat (olive oil) is a liquid), but branched GDGTs have not yet been identified as the main membrane lipids in Acidobacteria cultures. Thus their exact provenance is unknown.
Calibration of branched GDGTs to environmental variables (temperature, pH, salinity, precipitation, etc.) is a topic of widespread research. Organic geochemistry laboratories all over the world are involved in the task of developing both global1,10&#160;and regional11-13&#160;calibrations between branched GDGTs and (primarily) temperature. Thus, the equations given above are regularly being refined and perfected.
Branched GDGTs are usually extracted from lacustrine sediments, although coastal marine sediments have also been investigated. The extracts undergo a silica gel column to purify the GDGTs from other compounds which may not be LC amenable or that may co-elute with GDGTs chromatographically. The GDGTs come out in the polar fraction that elutes in methanol.
Once the total lipid extract is purified, the extracted and purified sample is run on a high performance liquid chromatograph coupled to a chemical ionization mass spectrometer. The relative concentration of the GDGTs is determined by obtaining the area under the curve for the selected mass ion (m/z; Figure 1) for each of the compounds on computer software designed for just this purpose (such as Agilent Chemstation). These areas are then put into the selected calibration equation in order to arrive at a paleotemperature determination.
<img alt="Figure 1" src="/files/ftp_upload/10256/10256fig1.jpg" /> 
Figure 1. Structures of the branched GDGTs used for calculating temperature via MBT/CBT proxy (used with permission of Dr. Isla Casta&#241;eda, who produced the image). <a href="https://www.jove.com/files/ftp_upload/10256/10256fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<div class="chapter_text" id="script_0">
Organic compounds called biomarkers can be used in Earth Science as paleothermometers to relate information on climates and environments of the past.
Living organisms produce these biomarkers, which provide us with information about the environment in which they lived. They can act as a proxy to tell us information about past events, like the Earth&#8217;s temperature millions of years ago.
Terrestrial paleotemperature can be analyzed using biomarkers found in sediment from fresh-water basins. One key class of these biomarkers are branched glycerol dialkyl glycerol tetraethers, or branched GDGTs.
This video will introduce the area of study, called paleoclimatology, which investigates past changes in fresh-water environments over hundreds of millions of year. This helps elucidate current and future climate and environmental changes.
</div>
<div class="chapter_text" id="script_1">
Sediments accumulate over geologic time, due to fluid movement and gravity, in sedimentary basins, or low areas in the Earth&#8217;s crust. Sedimentary basins include oceans, which collect marine sediment, or lakes, which collect lacustrine sediment. Marine and lacustrine basins contain different types of organisms, driven in large part by the difference in salinity between them. Thus, marine and lacustrine basins contain different biomarkers.
Branched GDGTs are thought to be membrane-spanning lipids of anaerobic acidobacteria. Research suggests that the producing organisms change membrane properties in response to changing temperature.
This change is caused by the transformation of methylated sites on the branched GDGT&#8217;s to cyclized sites at colder temperatures, thereby enhancing membrane fluidity. This change in structure can then be correlated to temperature through a proxy. Proxies are measureable physical phenomena that are correlated to immeasurable variable.
This proxy relates the number of methylations or MBT, and cyclizations, or CBT, in the biomarker to temperature. An experimentally-derived equation can relate MBT and CBT to the past Mean Annual Air Temperature.
</div>
<div class="chapter_text" id="script_2">
To study the relationship between branched GDGT biomarkers and soil temperature, lacustrine sediment must be collected, extracted by one of three techniques, purified, and analyzed.
To begin studying the relationship between branched GDGT biomarkers and soil temperature, the lipid molecules are first extracted from lacustrine sediments, using a variety of techniques. Extraction via sonication is the simplest and least expensive method of obtaining the total lipid extract, or TLE, from a sediment sample. For this, an ultrasonic bath is used to agitate the sample in a vial containing organic solvent. A mixture of methanol and dichloromethane is used to extract biomarkers with a wide range of polarities. Another extraction technique utilizes Soxhlet extraction. A Soxhlet extractor enables the reflux, or continuous cycling, of organic solvent from a round-bottom flask upward into a condenser, which is cooled by cold water and returned. The condensed solvent falls into a glass fiber thimble containing the sample. Once full, the chamber siphons the organic solvent back into the round-bottom flask, enabling continuous extraction over time.
This technique is helpful in the extraction of large sediment masses, and the preparation of large volumes of standards for instrument calibration. Finally, accelerated solvent extraction, or ASE, is a trademarked method of extraction that utilizes high temperature and pressure to increase the kinetics of the extraction process. The ASE instrument holds up to 24 individual samples, and allows for precise control of all parameters in the extraction process. Due to its speed and simplicity of use, ASE is commonly used as the standard method of solvent extraction.
</div>
<div class="chapter_text" id="script_3">
Once the lipid sample is extracted using one of these techniques, it is purified in preparation for analysis. Typically, silica gel column chromatography is used to purify the lipid sample based on its polarity. For this, a small glass column is loaded with a fine powder of silica, called a gel. The column is then saturated with an apolar solvent, typically hexane, and then the sample loaded on the top. The separation of the extract is based on the affinity of the target compound for either the solid phase or the solvent phase.
Polar compounds, in this case branched GDGT&#39;s, are more attracted to the polar silica than the apolar hexane. Thus, the apolar compounds, such as hydrocarbons, the mid-polar compounds, such as ketones and alcohols, and the highly polar compounds, will travel the column at different rates and in response to solvents of increasing polarity.
The eluents are then collected in separate fractions.
The purified GDGT&#39;s are then analyzed using high performance liquid chromatography coupled to a mass spectrometer, or LC-MS. LC-MS first separates the compounds, and then analyzes them based on their mass-to-charge ratio.
This enables the determination of the relative concentration of each type of GDGT using the area under the curve for the selected mass ion. MBT is calculated as the fraction of the group 1 molecules to the total.
CBT is then calculated as a negative log using molecules in groups 1 and 2. MBT and CBT are then plugged into an experimentally-derived equation, in order to arrive at a paleotemperature determination.
</div>
<div class="chapter_text" id="script_4">
The determination of paleotemperature using biomarker proxies is useful in a range of applications in earth science.
First, paleothermometry enables the determination of the Earth&#39;s temperature over long periods of time. Using various techniques, the temperature of Earth has been estimated as far back as 500 million years. This tells us the envelope of temperature within which different forms of life evolved and informs investigations of the effects of temperature on Earth&#39;s biosphere, hydrosphere, lithosphere, and atmosphere in the past, and by extension, the future.
More recent trends in the Earths temperature can also be quantified against records constructed using paleothermometry. The Earths surface temperature has increased by nearly 1 degree from 1850 to the present with an accentuated warming trend in the last two decades. To understand the anthropogenic impact on global climate, accurate paleoclimate records must be developed and used as context.
</div>
<div class="chapter_text" id="script_5">
You&#39;ve just watched JoVE&#39;s Overview of Branched Glycerol Dialkyl Glycerol Tetraether Paleothermometry. You should now understand how the branched GDGT biomarkers are used, and the overall technique of extracting and purifying them. The following videos in this series will go into more detail about this complex process.
Thanks for watching!
</div>

Source: Laboratory of Jeff Salacup&#160;- University of Massachusetts Amherst
Throughout this series of videos, natural samples were extracted and ...

JoVE Science Education

Environmental Sciences

Earth Science

What is Climate?

Climate refers to the prevailing weather conditions in a specific area over an extended period. As the saying goes, &ldquo;Climate is what you expect. Weather is what you get.&rdquo; Climate is influenced by geographic factors, such as latitude, terrain, and proximity to bodies of water.

<h4>Weather and Climate</h4>

Weather and climate are related, though they differ in terms of time scale and predictability. Weather refers to the state of the atmosphere at a specific time and place, whereas climate encompasses the &ldquo;average&rdquo; weather conditions over a much longer time. In terms of predictability, weather forecasts are limited to days, but the climate can be modeled and predicted over substantial periods, such as years or even decades.

<h4>The Climate System</h4>

The Earth&rsquo;s climate system consists of several smaller, interacting sub-systems. The atmosphere is an envelope of gases surrounding the Earth. The hydrosphere consists of all the water on, above, or below the Earth&rsquo;s surface. Oceans cover more than two-thirds of the Earth&rsquo;s surface. Ice, including sea ice, glaciers, ice sheets, and snow, comprises the cryosphere, which is also part of the hydrosphere. The geosphere, or lithosphere, consists of the Earth&rsquo;s crust. Finally, the biosphere includes all the ecosystems on Earth, including all living organisms and their interactions with the atmosphere, hydrosphere, cryosphere, and lithosphere. These sub-systems exchange energy, water, and momentum. The power source driving all of these complex interactions is radiation from the sun.

<h4>Planetary Energy Balance</h4>

The climate system is powered by radiation from the sun; however, solar radiation does not even provide enough energy to keep the Earth above freezing temperatures. The Earth&rsquo;s temperature, which has a significant impact on climate, depends on the amplification of thermal energy from solar radiation. The Earth&rsquo;s surface absorbs approximately 49% of solar radiation, and ~20% is absorbed by the atmosphere. This radiation warms the planet, which in turn causes the Earth to radiate energy back into space. Thus, the ultimate temperature of the planet is determined by the balance between the energy that as absorbed and lost.

<h4>Climate Change and Society</h4>

Compared to patterns revealed by historical data, Earth&rsquo;s climate is currently changing rapidly. While these changes are too minute to notice on a day-to-day basis, the accumulation of these minute changes could have devastating impacts on society. Agriculture and food production industries are particularly vulnerable to climate change, and several models have been created to predict the potential effects of climate change. While the effects of climate change on food production vary by crop and region, one model predicts that South Asia and Southern Africa are likely to suffer negative impacts on several crops that are important to large, food-insecure populations.

Climate and Seasons: Geographical Variations

Climate refers to the prevailing weather conditions in a specific area over an extended period. As the saying goes, &ldquo;Climate is what you expect. ...

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Biodiversity and Conservation

KEY TERMS AND CONCEPTS

Global Climate Change

Throughout its ~4.5 billion year history, the Earth has experienced periods of warming and cooling. However, the current drastic increase in global temperatures is well outside of the Earth&rsquo;s cyclic norms, and evidence for human-caused global climate change is compelling. Paleoclimatology, the study of ancient climate conditions, provides ample evidence for human-caused global climate change by comparing recent conditions with those in the past.

<h4>Past Periods of Warming and Cooling</h4>

In the last 650,000 years alone, there have been seven cycles of glacial advance and retreat. Over 11,000 years ago, the most recent ice age abruptly ended&mdash;marking the beginning of our modern climate era, the Holocene geological epoch. Most historical climate changes are associated with small variations in earth&rsquo;s orbit that changed the amount of the solar radiation received by the Earth.

<h4>Paleoclimatology</h4>

Paleoclimatology is the study of climatic conditions and their causes and effects throughout the Earth&rsquo;s geologic past. Paleoclimatologists employ a variety of scientific methods to deduce the past conditions of Earth&rsquo;s climate and atmospheric system.

<h4>Ice Core Data</h4>

Ice core samples taken from thick mountain glaciers and polar ice sheets can reveal information about global climate change. Seasonal pauses in ice accumulation can lead to observable layers in ice cores. These layers can be used to establish a chronology, with the lowest layers being the oldest. Researchers can then analyze properties of the ice and the material trapped inside it (e.g., air bubbles and ratios of oxygen and hydrogen isotopes) to reconstruct the Earth&rsquo;s ancient climate. The European Project for Ice Coring in Antarctica analyzed volcanic ash trapped in ice cores from Antarctica to provide a detailed record of Holocene volcanic history. This record revealed 96 eruptions during the Holocene, with 33 of those eruptions occurring during the last 2,000 years.

<h4>Dendroclimatology</h4>

Scientists can also study past climate by examining annual tree rings&mdash;a field called dendroclimatology. Essentially, tree rings are wider under favorable conditions and narrower during harsh times. Tree rings can be accurately dated by matching rings from sample to sample&mdash;even samples from archaeological digs. Although dendroclimatology has limitations, tree rings are useful climate proxies that can be used to create high-resolution climate records for specific geographic locations.

Global Warming and Climate Change

Throughout its ~4.5 billion year history, the Earth has experienced periods of warming and cooling. However, the current drastic increase in global ...

Using Generative Art to Convey Past and Future Climate Transitions

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