tag:theconversation.com,2011:/us/topics/green-fluorescent-protein-6186/articlesGreen fluorescent protein – The Conversation2021-08-05T12:48:25Ztag:theconversation.com,2011:article/1644592021-08-05T12:48:25Z2021-08-05T12:48:25ZFrom CRISPR to glowing proteins to optogenetics – scientists’ most powerful technologies have been borrowed from nature<figure><img src="https://images.theconversation.com/files/414624/original/file-20210804-15-1fuewod.jpg?ixlib=rb-1.1.0&rect=391%2C30%2C3002%2C1822&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Crystal jellyfish contain glowing proteins that scientists repurpose for an endless array of studies.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/crystal-jellyfish-royalty-free-image/1013185852?adppopup=true">Weili Li/Moment via Getty Images</a></span></figcaption></figure><p><a href="https://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397/">Watson and Crick</a>, <a href="https://www.nobelprize.org/prizes/physics/1933/schrodinger/biographical/">Schrödinger</a> and <a href="https://www.nobelprize.org/prizes/physics/1921/einstein/biographical/">Einstein</a> all made theoretical breakthroughs that have changed the world’s understanding of science. </p>
<p>Today big, game-changing ideas are less common. New and improved techniques are the <a href="https://doi.org/10.1038/nmeth1004-1">driving force behind modern scientific research and discoveries</a>. They allow scientists – <a href="https://scholar.google.com/citations?user=RpiSPiwAAAAJ&hl=en&oi=ao">including chemists like me</a> – to do our experiments faster than before, and they shine light on areas of science hidden to our predecessors. </p>
<p>Three cutting-edge techniques – the gene-editing tool <a href="https://www.newscientist.com/definition/what-is-crispr/">CRISPR</a>, <a href="https://doi.org/10.1242/jcs.072744">fluorescent proteins</a> and <a href="https://www.scientificamerican.com/article/optogenetics-controlling/">optogenetics</a> – were all inspired by nature. Biomolecular tools that have worked for bacteria, jellyfish and algae for millions of years are now being used in medicine and biological research. Directly or indirectly, they will change the lives of everyday people.</p>
<h2>Bacterial defense systems as genetic editors</h2>
<p>Bacteria and viruses battle themselves and one another. They are at constant biochemical war, <a href="https://doi.org/10.1016/j.cub.2019.04.024">competing for scarce resources</a>. </p>
<p>One of the weapons that bacteria have in their arsenal is the <a href="https://www.livescience.com/58790-crispr-explained.html">CRISPR-Cas system</a>. It is a genetic library consisting of short repeats of DNA gathered over time from hostile viruses, paired with a protein called Cas that can cut viral DNA as if with scissors. In the natural world, when bacteria are attacked by viruses whose DNA has been stored in the CRISPR archive, the CRISPR-Cas system hunts down, cuts and destroys the viral DNA.</p>
<p>Scientists have repurposed these weapons for their own use, with groundbreaking effect. Jennifer Doudna, a biochemist based at the University of California, Berkeley, and French microbiologist Emmanuelle Charpentier shared the <a href="https://theconversation.com/nobel-prize-for-chemistry-honors-exquisitely-precise-gene-editing-technique-crispr-a-gene-engineer-explains-how-it-works-147701">2020 Nobel Prize in chemistry</a> for <a href="https://www.nobelprize.org/prizes/chemistry/2020/doudna/lecture/">the development of</a> <a href="https://theconversation.com/nobel-prize-for-crispr-honors-two-great-scientists-and-leaves-out-many-others-147730">CRISPR-Cas as a gene-editing technique</a>. </p>
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<a href="https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="French researcher Emmanuelle Charpentier (left) and U.S. biochemist Jennifer Doudna (right)" src="https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=365&fit=crop&dpr=1 600w, https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=365&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=365&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=459&fit=crop&dpr=1 754w, https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=459&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/414580/original/file-20210804-21-1k8hfpd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=459&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">French microbiologist Emmanuelle Charpentier (left) and U.S. biochemist Jennifer Doudna shared the 2020 Nobel Prize in Chemistry for development of the CRISPR-Cas gene editing technique.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/french-researcher-in-microbiology-genetics-and-biochemistry-news-photo/493945408?adppopup=true">Miguel Riopa/AFP via Getty Images</a></span>
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<p>The <a href="https://www.genome.gov/human-genome-project">Human Genome Project</a> has provided a nearly complete genetic sequence for humans and given scientists a template to sequence all other organisms. However, before CRISPR-Cas, we researchers didn’t have the tools to easily access and edit the genes in living organisms. Today, thanks to CRISPR-Cas, lab work that used to take months and years and cost hundreds of thousands of dollars can be done in less than a week for just a few hundred dollars. </p>
<p>There are more than 10,000 genetic disorders caused by mutations that occur on only one gene, the <a href="http://hihg.med.miami.edu/thromboticstorm/genetics-overview/single-gene-disorders">so-called single-gene disorders</a>. They affect millions of people. <a href="https://www.genome.gov/Genetic-Disorders/Sickle-Cell-Disease">Sickle cell anemia</a>, <a href="https://www.cff.org/What-is-CF/Genetics/CF-Genetics-The-Basics/">cystic fibrosis</a> and <a href="https://doi.org/10.31887/DCNS.2016.18.1/pnopoulos">Huntington’s disease</a> are among the most well-known of these disorders. These are all obvious targets for CRISPR therapy because it is much simpler to fix or replace just one defective gene rather than needing to correct errors on multiple genes. </p>
<p>For example, in preclinical studies, <a href="https://doi.org/10.1056/NEJMoa2107454">researchers injected</a> an encapsuled CRISPR system into patients born with a rare genetic disease, <a href="https://rarediseases.info.nih.gov/diseases/656/familial-transthyretin-amyloidosis">transthyretin amyloidosis</a>, that causes fatal nerve and heart conditions. Preliminary results from the study demonstrated <a href="https://www.nature.com/articles/d41586-021-01776-4">that CRISPR-Cas can be injected</a> directly into patients in such a way that it can find and edit the faulty genes associated with a disease. In the six patients included in this landmark work, the encapsuled CRISPR-Cas minimissiles reached their target genes and did their job, causing a significant drop in a <a href="https://www.nature.com/scitable/topicpage/protein-misfolding-and-degenerative-diseases-14434929/">misfolded protein</a> associated with the disease. </p>
<h2>Jellyfish light up the microscopic world</h2>
<p>The <a href="https://faculty.washington.edu/cemills/Aequorea.html">crystal jellyfish, <em>Aequorea victoria</em></a>, which drifts aimlessly in the northern Pacific, has no brain, no anus and no poisonous stingers. It is an unlikely candidate to ignite a revolution in biotechnology. Yet on the periphery of its umbrella, it has about 300 photo-organs that give off pinpricks of green light that have changed the way science is conducted.</p>
<p>This bioluminescent light in the jellyfish stems from a luminescent protein called aequorin and a fluorescent molecule called <a href="https://doi.org/10.1242/jcs.072744">green fluorescent protein</a>, or GFP. In modern biotechnology GFP acts as a molecular lightbulb that can be fused to other proteins, allowing researchers to track them and to see when and where proteins are being made in the cells of living organisms. Fluorescent protein technology is used in thousands of labs every day and has resulted in the awarding of two Nobel Prizes, <a href="https://www.nobelprize.org/prizes/chemistry/2008/popular-information/">one in 2008</a> and the <a href="https://www.nobelprize.org/prizes/chemistry/2014/summary/">other in 2014</a>. And fluorescent proteins have now been found in <a href="https://doi.org/10.1242/jcs.072744">many more species</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Fluorescent bacteria in petri dish and test tube" src="https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/414422/original/file-20210803-13-vphczn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Fluorescent proteins, shown here glowing inside <em>E. coli</em> bacteria, allow researchers to visualize biological structures and processes.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/red-and-green-fluorescent-proteins-in-escherichia-royalty-free-image/124368916?adppopup=true">Fernan Federici/Moment via Getty Images</a></span>
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<p>This technology proved its utility once again when researchers created genetically modified <a href="https://doi.org/10.1016/j.cell.2020.05.042">COVID-19 viruses that express GFP</a>. The resulting fluorescence makes it possible to follow the path of the viruses as they enter the respiratory system and bind to surface cells with hairlike structures. </p>
<h2>Algae let us play the brain neuron by neuron</h2>
<p>When algae, which depend on sunlight for growth, are placed in a large aquarium in a darkened room, they swim around aimlessly. But if a lamp is turned on, the algae will swim toward the light. The single-celled <a href="https://www.britannica.com/science/flagellate">flagellates</a> – so named for the whiplike appendages they use to move around – don’t have eyes. Instead, they have a structure called an eyespot that distinguishes between light and darkness. The eyespot is studded with <a href="https://doi.org/10.1073/pnas.1525538113">light-sensitive proteins called channelrhodopsins</a>. </p>
<p>In the early 2000s, <a href="https://doi.org/10.1038/nn1525">researchers discovered</a> that when they genetically inserted these channelrhodopsins into the nerve cells of any organism, illuminating the channelrhodopsins with blue light caused neurons to fire. This technique, known as optogenetics, involves inserting the algae gene that makes channelrhodopsin into neurons. When a pinpoint beam of blue light is shined on these neurons, the channelrhodopsins open up, calcium ions flood through the neurons and the neurons fire. </p>
<p>Using this tool, scientists can stimulate groups of neurons selectively and repeatedly, thereby gaining a more precise understanding of which neurons to target to treat specific disorders and diseases. Optogenetics might hold the key to treating debilitating and deadly brain diseases, such as Alzheimer’s and Parkinson’s. </p>
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<a href="https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Illustration of amyloid plaque buildup on cells" src="https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/414426/original/file-20210803-25-1p9rv2y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Optogenetics could help treat Alzheimer’s disease, which is characterized by the buildup of misfolded proteins called amyloid plaques.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/illustration/illustration-of-alzheimers-disease-royalty-free-illustration/1124681623?adppopup=true">Sciepro/Science Photo Library via Getty Images</a></span>
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<p>But optogenetics isn’t only useful for understanding the brain. Researchers have used optogenetic techniques <a href="https://doi.org/10.1038/s41591-021-01351-4">to partially reverse blindness</a> and have found promising results in clinical trials using optogenetics on patients with <a href="https://www.nei.nih.gov/learn-about-eye-health/eye-conditions-and-diseases/retinitis-pigmentosa">retinitis pigmentosa</a>, a group of genetic disorders that break down retinal cells. And in mouse studies, the technique has been used to <a href="https://doi.org/10.1016/j.pbiomolbio.2019.08.013">manipulate heartbeat</a> and <a href="https://doi.org/10.1016/j.autneu.2020.102733">regulate bowel movements of constipated mice</a>. </p>
<h2>What else lies within nature’s toolbox?</h2>
<p>What undiscovered techniques does nature still hold for us? </p>
<p>According to <a href="https://doi.org/10.1073/pnas.1711842115">a 2018 study</a>, people represent just 0.01% of all living things by mass but have caused the loss of 83% of all wild mammals and half of all plants in our brief time on Earth. By annihilating nature, humankind might be losing out on new, powerful and life-altering techniques without having even imagined them.</p>
<p>[<em>Over 100,000 readers rely on The Conversation’s newsletter to understand the world.</em> <a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=100Ksignup">Sign up today</a>.]</p>
<p>After all, no one could have foreseen that the discovery of three groundbreaking processes derived from nature could change the way science is done.</p><img src="https://counter.theconversation.com/content/164459/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marc Zimmer received funding from NIH for his fluorescent protein research. </span></em></p>Three pioneering technologies have forever altered how researchers do their work and promise to revolutionize medicine, from correcting genetic disorders to treating degenerative brain diseases.Marc Zimmer, Professor of Chemistry, Connecticut CollegeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1004352018-08-07T10:40:25Z2018-08-07T10:40:25ZFunding basic research plays the long game for future payoffs<figure><img src="https://images.theconversation.com/files/230804/original/file-20180806-191013-1fnl7ab.jpg?ixlib=rb-1.1.0&rect=429%2C222%2C3660%2C2667&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">It takes time to see which finding might be a golden egg.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/one-gold-egg-lays-among-common-111414110">Neamov/Shutterstock.com</a></span></figcaption></figure><p>The Senate recently proposed to increase the research budgets of the <a href="http://www.sciencemag.org/news/2018/06/senate-panel-proposes-2-billion-54-increase-nih">National Institutes of Health</a>, <a href="http://www.sciencemag.org/news/2018/06/nasa-science-and-nsf-do-well-senate-spending-bill">National Science Foundation and NASA</a>. While this is encouraging to the many scientists whose research is dependent on grants from these agencies, it comes at a time when scientific research is under increased scrutiny.</p>
<p>Questioning the merit of scientific research is certainly not new. In the 1970s and 1980s the <a href="https://www.wisconsinhistory.org/turningpoints/search.asp?id=1742">Golden Fleece Awards</a> were an ignominious honor bestowed by a U.S. senator on what he considered “wasteful” research. The majority of the ire was aimed at research thought to be “useless.” </p>
<p>But having no obvious immediate application <a href="https://theconversation.com/tracing-the-links-between-basic-research-and-real-world-applications-82198">doesn’t mean something will never be of use</a>.</p>
<p>Perhaps the difficultly in justifying basic research is in part a branding problem. The goal of this type of work is to understand the fundamental principles of nature, and it spans the STEM fields (Science, Technology, Engineering and Mathematics). Once these fundamental principles are understood, they can be applied to more translational research that can have direct benefits to patients or consumers. </p>
<p>But the benefits of basic research are often not instantly recognizable. Potential long-term payoffs – perhaps ones that haven’t even been imagined yet – won’t help consumers or patients now.</p>
<p>There are countless discoveries whose eventual impact would have been very difficult to predict when the research was in its infancy. Honors like the <a href="https://www.goldengooseaward.org/">Golden Goose Award</a>, presented every fall since 2012, combat the idea of basic research being “wasteful” or “useless” by underscoring that it’s actually the foundation for further scientific innovation. Given enough time and support, basic research can yield significant real-world benefits that were hard to predict in advance. Here are two examples of scientific curiosity paying substantial dividends decades after the initial discovery.</p>
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<a href="https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/230806/original/file-20180806-34489-1u0hpnh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">What could a bioluminescent jellyfish contribute to medical science?</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/crystal-jellyfish-aequorea-victoria-bioluminescent-hydrozoan-671090275">LagunaticPhoto/Shutterstock.com</a></span>
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<h2>From glowing jellyfish to biomedical imaging</h2>
<p>It was very unlikely that scientists were thinking of medical applications when in the 1950s they started studying why some <a href="https://doi.org/10.1098/rspb.1955.0066">jellyfish glow</a>. Marine biologists discovered that the jellyfish <em>Aequorea victoria</em> was <a href="https://ocean.si.edu/ocean-life/fish/bioluminescence">bioluminescent</a>. What was unclear at the time was how this jellyfish produces its light, which is a vibrant green color.</p>
<p>Seven years later a group of researchers discovered that the living light from the jellyfish came from a single protein they called <a href="https://doi.org/10.1002/jcp.1030590302">aequorin</a>. Strangely, the light from the purified aequorin protein was blue, not green. After another eight years of work they found that a partner protein to aequorin, which they called green fluorescent protein (<a href="https://doi.org/10.1002/jcp.1040770305">GFP</a>), produced the vibrant green-colored light seen in the living jellyfish.</p>
<p>The question then became how did the two proteins work together to produce this light? It took another 10 years of work to get the answer. A series of papers published in the early 1970s characterized a small molecule called a <a href="https://doi.org/10.2144/000113765">chromophore</a> that integrated into the <a href="https://doi.org/10.1016/0014-5793(79)80818-2">GFP protein structure</a>. The <a href="https://doi.org/10.1126/science.273.5280.1392">structure of GFP</a> was discovered in the early 1990s, which further helped researchers understand how this protein created light in living cells.</p>
<p>The first time the GFP protein was produced in an organism other than a jellyfish was in 1992. Expressing GFP in the small worm <em>C. elegans</em> and the bacterium <em>E. coli</em> <a href="https://doi.org/10.1126/science.8303295">made them both glow</a> a brilliant green color. This breakthrough, nearly 40 years after the initial jellyfish study, opened the door for using GFP as powerful tool for biomedical research. Today researchers use GFP to track protein interactions and movement in living cells, which is useful in the study of cancer and bacterial diseases. A current literature search in PubMed returns over 30,000 peer-reviewed published papers using the search term “<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=%22green+fluorescent+protein%22">green fluorescent protein</a>.”</p>
<p>The impact of GFP has also been recognized with a <a href="https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2008/advanced-chemistryprize2008.pdf">Nobel Prize</a> in 2008 and an inaugural Golden Goose Award in 2012.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/230807/original/file-20180806-191031-1y0ysvs.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">What could a bacteria’s immune system add to genetic researchers’ toolkit?</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/3d-illustration-crisprcas13a-system-1029539410">Meletios Verras/Shutterstock.com</a></span>
</figcaption>
</figure>
<h2>From bacterial immunity to genome editing</h2>
<p>A more recent example of how basic research is now driving incredible innovation can be found in the fields of synthetic biology and genome editing, thanks to what actually started out very humbly as the characterization of bacteria. In the late 1980s, researchers found that certain bacteria had <a href="https://doi.org/10.1128/jb.169.12.5429-5433.1987">short repeated regions</a> in their genome, but they didn’t know their purpose. They called these DNA sequences Clustered Regularly Interspaced Short Palindromic Repeats; you’ve probably heard its acronym nickname <a href="https://doi.org/10.1046/j.1365-2958.2002.02839.x">CRISPR</a>. Work characterizing and cataloging bacteria that had these short repeated sequences continued for 20 years before researchers discovered proteins associated with the short DNA repeats. They called them CRISPR associated, or Cas, proteins.</p>
<p>One major advance happened in 2005 when researchers realized that CRISPR sequences found in bacterial genomes <a href="https://doi.org/10.1099/mic.0.28048-0">match DNA in phages</a>, viruses that infect bacteria. A few more years later, scientists showed that the CRISPR-Cas system was a type of <a href="https://doi.org/10.1126/science.1138140">adaptive immunity</a> that bacteria use to remember phage infection and prevent it from happening again. The Cas protein cuts invading phage’s DNA to stop infection. This discovery was groundbreaking; no one had known something as simple as a single-celled bacterium could have a sophisticated immune system.</p>
<p>And then in 2013, researchers realized this type of directed DNA cutting could be used to <a href="https://doi.org/10.1126/science.1231143">edit the genomes of other organisms</a>, not just bacteria. The method was quickly adapted for use in yeast, worm, fruit fly, zebrafish, mouse, plant and human cells. Genome editing in this way will have far-reaching implications for everything from food production to stem cell therapies.</p>
<p>Thirty years after its discovery, the scope of CRISPR research is truly impressive; a current literature search in PubMed returns over 10,000 peer-reviewed published papers using the search term “<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=CRISPR">CRISPR</a>.” The technologies stemming from CRISPR have not won a Golden Goose Award or Nobel Prize yet, but some speculate it is only a <a href="http://blogs.plos.org/synbio/2017/10/05/when-will-crispr-get-a-nobel-prize/">matter of time</a>.</p>
<h2>Curiosity and patience yield dividends</h2>
<p>Answering fundamental questions – Why do jellyfish glow? Why do bacterial genomes have short repeating DNA sequences? – <a href="https://www.goldengooseaward.org/awardees/">can lead to innovation and tangible benefits</a> in many aspects of everyday life. And a Golden Goose Award or Nobel Prize is not required to show that a discovery has translational application. An entrepreneurship study published in 2017 highlighted that more than 75 percent of research articles published are <a href="https://doi.org/10.1126/science.aam9527">eventually referenced in at least one patent disclosure</a>. This study showed a strong link between patent applications, ostensibly a quantitative metric of innovation, and basic research taking place at universities and government laboratories. </p>
<p>Real-world impacts stemming from basic research can take decades to unfold. If basic science is not supported and funded in the U.S., other countries will take over the innovation leadership role. Much like the goose that laid golden eggs, time and patience are required to get the most out of basic research.</p><img src="https://counter.theconversation.com/content/100435/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jeffrey Gardner receives funding from the US Department of Energy. </span></em></p>Basic research can be easy to mock as pointless and wasteful of resources. But it’s very often the foundation for future innovation – even in ways the original scientists couldn’t have imagined.Jeffrey Gardner, Associate Professor of Biological Sciences, University of Maryland, Baltimore CountyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/450322015-08-07T10:03:40Z2015-08-07T10:03:40ZTaking plants off planet – how do they grow in zero gravity?<figure><img src="https://images.theconversation.com/files/91081/original/image-20150806-5209-8ine5y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Astronaut Cady Coleman harvests one of our plants on Space Shuttle Columbia.</span> <span class="attribution"><span class="source">NASA</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>Gravity is a constant for all organisms on Earth. It acts on every aspect of our physiology, behavior and development – no matter what you are, you evolved in an environment where gravity roots us firmly to the ground.</p>
<p>But what happens if you’re removed from that familiar environment and placed into a situation outside your evolutionary experience? That’s exactly the question we ask every day of the plants we grow <a href="http://ufspaceplants.org/">in our laboratory</a>. They start out here in our earthbound lab, but they’re on their way to outer space. What could be a more novel environment for a plant than the zero-gravity conditions of spaceflight?</p>
<p>By studying how plants react to life in space, we can learn more about how they adapt to environmental changes. Not only are plants crucial to almost every facet of life on Earth; plants will be critical to our explorations of the universe. As we look to a future of possible space colonization, it’s vital to understand how plants will fare off planet before we rely on them within space outposts to recycle our air and water and supplement our food.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=410&fit=crop&dpr=1 600w, https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=410&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=410&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=515&fit=crop&dpr=1 754w, https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=515&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/91057/original/image-20150806-5245-f4vboc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=515&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Astronaut Jeff Williams harvests our Arabidopsis plants on the ISS.</span>
<span class="attribution"><span class="source">NASA</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>So even while we stay right here on the ground, <a href="http://www.nasa.gov/mission_pages/station/research/experiments/709.html">our research plants</a> blast off and head to the <a href="http://www.nasa.gov/mission_pages/station/main/index.html">International Space Station</a> (ISS). Already they’ve given us some surprises about growing in zero gravity – and shaken up some of our thinking about how plants grow on Earth.</p>
<h2>Learning from stressed-out plants</h2>
<p>Plants make especially great research subjects if you’re interested in environmental stress. Because they’re stuck in one spot – what we biologists call sessile organisms – plants must cleverly deal in place with whatever their environment throws at them. Moving to a more favorable spot isn’t an option, and they can do little to alter the environment around them.</p>
<p>But what they can do is alter their internal “environment” – and plants are masters of manipulating their metabolism to cope with perturbations of their surroundings. This characteristic is one of the reasons we use plants in our research; we can count on them to be sensitive reporters of environmental change, even in novel environments like spaceflight.</p>
<p>Folks have been curious about how plants respond to spaceflight from the very beginning of our ability to get there. We launched <a href="http://www.ncbi.nlm.nih.gov/pubmed/11402191">our first spaceflight experiment</a> on Space Shuttle Columbia back in 1999, and the things we learned then are still fueling new hypotheses about how plants deal with the absence of gravity.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/91054/original/image-20150806-5209-19h6t3u.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Authors Robert Ferl (front) and Anna-Lisa Paul (middle) conduct a plant experiment in the microgravity conditions of NASA’s parabolic flight aircraft.</span>
<span class="attribution"><span class="source">NASA</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>We’re in Florida, our research plants are in space</h2>
<p>Spaceflight requires specialized growth habitats, specialized tools for observation and sample collection, and of course specialized people to take care of the experiment on orbit.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=703&fit=crop&dpr=1 600w, https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=703&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=703&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=883&fit=crop&dpr=1 754w, https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=883&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/91052/original/image-20150806-5233-u2l6eq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=883&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The Advanced Biological Research System spaceflight hardware showing the Petri plates with plants.</span>
<span class="attribution"><span class="source">Anna-Lisa Paul</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>A typical experiment begins on Earth in our lab with the planting of dormant Arabidopsis seeds in Petri plates containing a nutrient gel. This gel (unlike soil) stays put in zero gravity, and provides the water and nutrients the growing plants will need. The plates are then wrapped in dark cloth, taken to Kennedy Space Center, and eventually loaded into the Dragon Capsule on top of a Falcon 9 rocket to catch a ride to the ISS.</p>
<p>Once docked, an astronaut inserts the plates into the plant growth hardware. The light inside stimulates the seeds to sprout, cameras record the growth of the seedlings over time, and at the end of the experiment, the astronaut harvests the 12-day-old plants and save them in tubes of preservative.</p>
<p>Once returned to us on Earth, we can run more tests on the preserved samples to investigate the unique metabolic processes the plants engaged while on orbit.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/91056/original/image-20150806-5233-1nalc12.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The imaging system we built with colleagues to capture fluorescent plant gene expression data during parabolic flight and, eventually, suborbital operations.</span>
<span class="attribution"><span class="source">Robert Ferl</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>Unraveling it back in the lab</h2>
<p>One of the first things we found was that certain root growth strategies that everyone had assumed need gravity actually don’t require it at all.</p>
<p>To seek out water and nutrients, plants need their roots to grow away from where they are planted. On Earth, gravity is the most important “cue” for the direction to grow, but plants also use touch (think of the root tip as a sensitive fingertip) to help navigate around obstacles.</p>
<p>Back in 1880, Charles Darwin showed that when you grow plants along a slanted surface, the roots don’t grow straight away from the seed, but rather take a jog to one side. This root growth strategy is called “skewing.” <a href="http://www.freeinfosociety.com/media/pdf/4790.pdf">Darwin hypothesized</a> that a combination of gravity and the root touching its way across the surface was behind it - and for 130 years, that’s what everyone else thought too.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/fF0eHg4aX_Y?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Roots grew with skew – without gravity.</span></figcaption>
</figure>
<p>But in 2010, we saw that the roots of the plants we grew on the ISS marched across the surface of their Petri plate in a <a href="http://dx.doi.org/10.1186/1471-2229-12-232">perfect example of root skewing</a> – no gravity required. It was quite a surprise. So what’s really behind root-skewing on orbit, since it’s obviously not gravity?</p>
<p>Plants on the ISS do have a potentially second source of information from which they could get a directional cue: light. We hypothesized that in the absence of gravity to point roots “away” from the direction of the leaves, light plays a bigger role in root guidance.</p>
<p>What we found was that yes, light is important, but not just any light will do – there has to be a gradient of light intensity for it to act as a useful guide. Think of it in terms of a good smell: you can navigate to the kitchen with your eyes closed when cookies are just coming out of the oven, but if the whole house is flooded equally with the scent of chocolate chip cookies, you couldn’t find your way.</p>
<h2>Adjusting their metabolic toolbox on the fly</h2>
<p>In the absence of gravity, plants can’t use the “tools” they’re used to for navigation, so they had to craft together another solution. They can do that by regulating the way they express their genes. That way they can make more or less of specific proteins that are helpful or not in zero gravity. Various plant parts came up with their own gene regulation strategies.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/IvmPc4j25ao?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Glowing plants let us see which genes are active, so we can tell which proteins are being made.</span></figcaption>
</figure>
<p>We found a number of genes involved in making and remodeling cell walls are <a href="http://dx.doi.org/10.1186/1471-2229-13-112">expressed differently</a> in space-grown plants. Other genes involved with light-sensing – normally expressed in leaves on Earth – are expressed in roots on the ISS. In leaves, many genes associated with plant hormone signaling are repressed, and genes associated with insect defense are more active. <a href="http://dx.doi.org/10.1089/ast.2014.1210">These same trends</a> are also seen in the relative abundance of proteins involved in signaling, cell wall metabolism and defense.</p>
<p>These patterns of genes and proteins tell a story – in microgravity, plants respond by loosening their cell walls, along with creating new ways to sense their environment.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=397&fit=crop&dpr=1 600w, https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=397&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=397&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=499&fit=crop&dpr=1 754w, https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=499&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/91055/original/image-20150806-5260-1vctak6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=499&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Engineered Arabidopsis plants. Green color shows where green fluorescent protein (GFP) is being expressed, and red shows the natural fluorescence of chlorophyll.</span>
<span class="attribution"><span class="source">Anna-Lisa Paul</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>We track these gene expression changes in real time by labeling specific proteins with a fluorescent tag. Plants engineered with <a href="https://theconversation.com/fluorescent-proteins-light-up-science-by-making-the-invisible-visible-39272">glowing fluorescent proteins</a> can then “report” how they are responding to their environment as it is happening. These engineered plants act as biological sensors – “biosensors” for short. Specialized cameras and microscopes let us follow how the plant is utilizing those fluorescent proteins.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/purGp-1juCE?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The authors inside the “Vomit Comet” that recreates microgravity conditions on Earth.</span></figcaption>
</figure>
<h2>Insights from space</h2>
<p>This kind of research gives us new understanding of how plants sense and respond to external stimuli at a fundamental, molecular level. The more we can learn about how plants respond to novel and extreme environments, the more prepared we are for understanding how plants will deal with the changing environments they’re up against here on Earth.</p>
<p>And of course our research will inform collective efforts to take our biology off the planet. The observation that gravity isn’t as vital to plants as we once thought is welcome news for the prospect of farming on other planets with low gravity, and even on spacecraft where there is no gravity. Humans are explorers, and when we leave earth’s orbit, you can bet we’ll take plants with us!</p><img src="https://counter.theconversation.com/content/45032/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anna-Lisa Paul receives funding from NASA research grants.</span></em></p><p class="fine-print"><em><span>Robert Ferl receives funding from NASA.</span></em></p>Plants on the International Space Station must figure out how to grow in a completely novel environment. Their adaptability hints at how they’ll react to changes here on Earth – or in future space outposts.Anna-Lisa Paul, Research Professor, Graduate Faculty in Plant Molecular and Cellular Biology, University of FloridaRobert Ferl, Director of the Interdisciplinary Center for Biotechnology Research, University of FloridaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/392722015-04-07T10:16:29Z2015-04-07T10:16:29ZFluorescent proteins light up science by making the invisible visible<figure><img src="https://images.theconversation.com/files/77059/original/image-20150403-9342-6eqpw2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Multiple fluorescent proteins illuminate the cells in a human brainstem.</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/wbur/2926259123">Jeff Lichtman/Harvard University</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span></figcaption></figure><p>When you look up at the blue sky, where are the stars that you see at night? They’re there but we can’t see them. A firefly flitting across a field is invisible to us during the day, but at night we can easily spot its flashes. Similarly, proteins, viruses, parasites and bacteria inside living cells can’t be seen by the naked eye under normal conditions. But a technique using a fluorescent protein can light up cells’ molecular machinations like a microscopic flashlight.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=911&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=911&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=911&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1144&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1144&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77052/original/image-20150403-9306-19yekgr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1144&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The crystal jellyfish has about 300 photo organs on the bottom edge of the jellyfish’s umbrella.</span>
<span class="attribution"><span class="source">Courtesy Steven Haddock – http://biolum.eemb.ucsb.edu</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>The first fluorescent protein found in nature comes from the crystal jellyfish, <em>Aequorea victoria</em>, where it is responsible for the green light emitted by its photo organs. It’s called green fluorescent protein (GFP). We don’t know why these jellyfish have this lit-up feature. </p>
<p>Fluorescent proteins absorb light with short wavelengths, such as blue light, and immediately return it with a different color light that has a longer wavelength, such as green. In <em>Aequorea victoria</em>, a protein named aequorin produces blue light which GFP converts into the green light emitted by the jellyfish’s photo organs. This visibility under standard conditions is extremely rare; most other organisms have fluorescent proteins that are only visible if they are illuminated by external blue light sources. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=647&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=647&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=647&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=812&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=812&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77053/original/image-20150403-9312-e4gcxw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=812&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Close up of a few of the photo organs.</span>
<span class="attribution"><span class="source">Courtesy Steven Haddock – http://biolum.eemb.ucsb.edu</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>After the green fluorescent jellyfish protein, many other fluorescent proteins have been both found in nature and created in the lab. We now have a spectrum of fluorescent colors available to us that make previously invisible biological structures and processes visible in blazing fluorescent glory. Many new applications reliant on these colors are being published on a regular basis.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77054/original/image-20150403-9335-1x9xk6w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Petri dish with bacterial colonies expressing differently colored fluorescent proteins. These fluorescent proteins developed by Roger Tsien’s group are called the mFruits and have names like mHoneydew, mTomato, mCherry, mRaspberry, and mPlum.</span>
<span class="attribution"><a class="source" href="http://en.wikipedia.org/wiki/File:FPbeachTsien.jpg">Paul Steinbach and Roger Y. Tsien, University of California, San Diego</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<h2>Shining a light on imaging</h2>
<p>Fluorescent protein technology has led to many other interesting developments designed to improve imaging with these glowing molecules.</p>
<p>CaMPARI is one new technique, short for calcium-modulated photoactivatable ratiometric integrator. By exploiting the fact that calcium concentrations change when nerve cells send signals, CaMPARI is able to <a href="http://dx.doi.org/10.1126/science.1260922">light up all the neurons that have fired</a> in a living organism. The technique is based on a fluorescent protein called EOS, which changes its fluorescence from green to red. In fruit flies, zebrafish and mice, CaMPARI-genetically-modified neurons fluoresce red if they are active and green if they are less active.</p>
<p>Before CaMPARI, all the fluorescent calcium indicators available temporarily lit up when the neuron fired. They couldn’t record the firing history of neurons or indicate whether a neuron had fired in the past. According to Loren Looger, one of the researchers who worked on the development of CaMPARI, “The most enabling thing about this technology may be that you don’t have to have your organism under a microscope during your experiment. So we can now <a href="http://www.hhmi.org/news/new-fluorescent-protein-permanently-marks-neurons-fire">visualize neural activity</a> in fly larvae crawling on a plate or fish swimming in a dish.”</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/c-NMfp13Uug?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The CLARITY technique removes opaque parts and makes the whole brain transparent.</span></figcaption>
</figure>
<h2>Expanding and transparent brains</h2>
<p>Even with the help of light emitted by fluorescent proteins, it’s difficult to image neurons tangled deep within the brain. Ed Boyden, a neuroscientist from MIT, has created a method to expand brains to make fluorescent neurons deep within the brain more visible. He uses acrylate, which forms a dense mesh to hold the brain in place and expand in the presence of water <a href="http://dx.doi.org/10.1126/science.1260088">thereby inflating the brain</a> equally by about 4.5 times in each direction. It’s a lot like a diaper expanding when it gets wet. Boyden thinks that this “expansion microscopy may provide a key tool for <a href="http://www.kurzweilai.net/expanding-the-brain-achieves-super-resolution-with-ordinary-confocal-microscopes">comprehensive, precise, circuit-wide, brain mapping</a>.”</p>
<p>One of the reasons expansion microscopy is so useful is that the brain can be made see-through before it is blown up several sizes larger. In 2013 Karl Deisseroth and Viviana Gradinaru at Stanford published a method called CLARITY that removes opaque molecules such as fats and <a href="http://dx.doi.org/10.1038/nature12107">makes the brain transparent</a> without changing its shape. According to Thomas Insel, director of the US National Institute of Mental Health, “This is probably one of the most <a href="http://dx.doi.org/10.1038/496151a">important advances for doing neuroanatomy</a> in decades.” Since developing CLARITY for brains, Gradinaru has extended the method to all other organs including <a href="http://dx.doi.org/10.1016/j.cell.2014.07.017">an entire mouse</a>.</p>
<p>Both of these methods can be applied to brains that have been genetically modified with fluorescent proteins, therefore allowing for the visualization of neurons deep within the brain.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=628&fit=crop&dpr=1 600w, https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=628&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=628&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=790&fit=crop&dpr=1 754w, https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=790&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/76988/original/image-20150402-9342-1lodej7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=790&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Mouse neurons labeled by GFPs.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/wellcomeimages/6880271634">Wellcome Images</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<p>In 2008, the three scientists responsible for taking GFP from the jellyfish and making it a common tool used in over a million experiments all over the world were awarded the <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2008/">100th Nobel Prize in chemistry</a>. And in 2014 three other scientists were awarded the Nobel Prize for using fluorescent protein to <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2014/">increase the resolution of light microscopes</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/76987/original/image-20150402-9306-wspqgb.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>E. coli</em> with GFPs glowing in their petri dishes.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/cdepaz/4979454151">Carlos de Paz</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></span>
</figcaption>
</figure>
<h2>Revolutionary and resilient</h2>
<p>I’ve been researching the photochemistry and photophysics of fluorescent proteins since they were first used in imaging technology in 1994, I’ve <a href="https://global.oup.com/academic/product/illuminating-disease-9780199362813?cc=us&lang=en&">written two books</a> on them, and still I’m stunned by the many different ways in which this fairly simple protein can be used. Perhaps I shouldn’t be surprised that plasmid DNA molecules coding for GFP have survived space flight – not inside the rocket, but on the outside where they were exposed to 1800F (1000C) temperatures and mad friction. 53% of the DNA intentionally placed inside the screw heads in the TEXUS-49 rocket mission <a href="http://dx.doi.org/10.1371/journal.pone.0112979">expressed fully fluorescent GFP</a> when inserted into cells upon return to earth.</p>
<p>Like stars at night, fluorescent proteins have been lighting up science for the last 20 years. And it won’t be long before they’re guiding surgeons to tumorous growths during surgery and allowing researchers to switch on and off selected biomolecular processes.</p><img src="https://counter.theconversation.com/content/39272/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marc Zimmer receives funding from NIH.</span></em></p>First found in jellyfish, but now inserted into all kinds of organisms, GFPs illuminate biological structures and processes that researchers otherwise couldn’t see.Marc Zimmer, Professor of Chemistry and author of Illuminating Disease, Connecticut CollegeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/191182013-10-17T14:17:01Z2013-10-17T14:17:01ZHow glow-in-the-dark jellyfish revolutionised plant biology<figure><img src="https://images.theconversation.com/files/33207/original/jvt8d3hy-1382016925.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Revealing secrets of plants</span> <span class="attribution"><span class="source">corruptkitten</span></span></figcaption></figure><p>What happens inside plant cells? How can we see proteins in living cells that aren’t even visible with a microscope? This was a problem in plant cell biology until the discovery of a fluorescent jellyfish and the isolation of the protein responsible for its green glow. Over the past half a century since the discovery of green fluorescent protein (GFP) biologists have gained the tools necessary to illuminate the microscopic world inside of a living cell.</p>
<p>Three scientists involved in the discovery and development of GFP received the Nobel Prize in Chemistry in 2008, reflecting how this work has revolutionised cell biology research. The protein and its derivatives have been harnessed as essential tools for studying life at a protein level. No longer confined to the jellyfish species <em>Aequorea victoria</em>, GFP can be found inside cells in research labs across the globe.</p>
<h2>Natural glow</h2>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/33094/original/347rj5s9-1381879478.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A tobacco cell expressing GFP-HDEL (GFP fused to the endoplasmic reticulum (ER) luminal marker HDEL).</span>
<span class="attribution"><span class="source">Petra Kiviniemi</span></span>
</figcaption>
</figure>
<p>In the early 1960s Osamu Shimomura arrived from Japan at Princeton University to study naturally glowing (bioluminescent) jellyfish. The species <em>Aequorea victoria</em> emitted a bright green glow and became the focus of their research. Several scientists including Shimomura travelled to Washington State where they used nets to collect, by hand, approximately 10,000 jellyfish, separating the outer ring containing the green light emitting segments and discarding the rest. They then ground the harvested parts and passed them through a cheese cloth to form what the team referred to as jellyfish “squeezate”. From this they isolated two proteins. The first was aequorin, which required calcium to produce bioluminescence. Unlike aequorin, the second protein required activation with ultraviolet (UV) light for the fluorescence. This protein was green fluorescent protein (GFP). The capacity of GFP to function without requiring other interacting molecules was a novel observation and over the following decades its potential for use in research was realised.</p>
<p>The gene for GFP was cloned from the jellyfish DNA in 1992 by Douglas Prasher. Two years later Martin Chalfie inserted this gene into the cells of a bacterium, <em>E. coli</em> and the roundworm <em>C. elegans</em>. When the cells were exposed to UV light they emitted a green fluorescence, as the protein had done on its own in a test tube in Shimomura’s laboratory.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/33095/original/5jkpb52q-1381879483.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A tobacco plant expressing GFP-HDEL in day light.</span>
<span class="attribution"><span class="source">Petra Kiviniemi</span></span>
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<p>This initial work proved the concept that the gene for GFP could be inserted into the genetic code of different species, who can then be made to make their own GFP. Mutated variants of the GFP molecule were developed by Roger Tsien to produce different wavelengths of light and therefore different colours of fluorescence. Processes that were never seen before, quite literally, illuminated and able to be analysed as they happen inside living cells.</p>
<p>Research methods employing GFP have become one of the most widely used by plant cell biologist. Combined with the other techniques such as fluorescent stains and a powerful range of microscopes, GFP has enabled us to build a clearer picture of protein function in cells than ever before. As with the first experiments using bacteria and flatworms, plant biologists use the GFP gene fused to genes for proteins of interest and insert this DNA into the plant cells. As this is carried out in living tissue, the movement of the protein inside of the cell, as well as the initial location, can be imaged and analysed. For example, we can label membrane proteins in order to see and understand how cellular membranes move in real time.</p>
<p>With these techniques research is building an increasingly complete picture of the intricate, immensely complex and coordinated protein activity constantly occurring inside of cells. </p><img src="https://counter.theconversation.com/content/19118/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Petra Kiviniemi does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>What happens inside plant cells? How can we see proteins in living cells that aren’t even visible with a microscope? This was a problem in plant cell biology until the discovery of a fluorescent jellyfish…Petra Kiviniemi, PhD Student, Oxford Brookes UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/154272013-06-25T13:25:44Z2013-06-25T13:25:44ZProtein from sushi snack may help detect liver diseases<figure><img src="https://images.theconversation.com/files/26163/original/xmvf35kx-1372156537.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The molecule that causes the eel to glow when blue light is shone on it is unlike any found in other living organisms.</span> <span class="attribution"><span class="source">Akiko Kumagai & Atsushi Miyawaki</span></span></figcaption></figure><p>Researchers have discovered a fluorescent protein in a Japanese eel consumed as a popular sushi snack. The discovery could help develop simpler and more sensitive tests to detect jaundice and other diseases.</p>
<p>The idiom “seeing is believing” has been revived by biologists through the use of fluorescence microscopy, where specifically tagged proteins glow green when a laser is shone on them. This green glow allows researchers to observe phenomena at very minute scales (at some billionths of a meter).</p>
<p>The importance of such proteins called green fluorescent proteins (GFPs) was recognised by the <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2008/">2008 Nobel Prize in Chemistry</a>. But so far all the GFPs have been derived from non-vertebrate animals - those that lack a spinal cord - such as jellyfish and corals.</p>
<p>The discovery of the new fluorescent protein, named UnaG after the Japanese eel unagi, is important not just because it comes from a vertebrate animal but also because it is very different from any of the GFPs currently available.</p>
<h2>A special glow</h2>
<p>The first GFP was discovered in a jellyfish called <em>Aequorea victoria</em> almost 50 years ago. Since then tiny tweaks to this GFP and others that were discovered later on have given researchers a reliable tool to probe how a cell works.</p>
<p>Uncovering the cell’s molecular machinery is key to developing new medicines and tools to diagnose diseases. The use of GFPs allows scientists to pinpoint a single class of proteins among thousands that are at work in a cell.</p>
<p>The results of the new discovery were published in the journal <a href="http://www.sciencedirect.com/science/article/pii/S0092867413006442">Cell</a> recently. A team led by Atsushi Miyawaki at the RIKEN Institute in Japan found UnaG when they were studying the muscle fibres of freshwater eels.</p>
<p>The protein was unique not just because it was found in a vertebrate animal, but also because of the way it fluoresced. Most GFPs use a chromophore, which is a part of the molecule that can absorb and emit light. Instead UnaG glows by integrating a molecule from outside the protein.</p>
<p>This molecule turns out to be bilirubin, which is present in eel muscles but is also formed when haemoglobin breaks down in human blood. Levels of bilirubin have been used for decades as a test to assess liver health and diagnose diseases such as jaundice. So this ability of UnaG gives it the potential to detect bilirubin and act as an indicator for liver malfunction.</p>
<p>Binding to bilirubin gives UnaG some more special properties that no other GFP currently has. First, it is only half the size of current GFPs, which makes it handy to tag proteins without interfering with their function. Second, most GFPs require oxygen to produce their chromophore and thus become fluorescent. UnaG does not. This means it could for the first time allow the illumination of cells in tissues where oxygen is scarce, such as some cancerous tumours.</p>
<p>Biology has always been driven by the ability to “see” nature. Modern tools have allowed scientists to see beyond what the naked eye could offer. And the race is on to see phenomena happening on <a href="https://theconversation.com/new-method-can-image-single-molecules-and-identify-its-atoms-14869">ever smaller scales</a>. UnaG is one big step in that direction.</p>
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<p class="fine-print"><em><span>Luc Henry does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Researchers have discovered a fluorescent protein in a Japanese eel consumed as a popular sushi snack. The discovery could help develop simpler and more sensitive tests to detect jaundice and other diseases…Luc Henry, Postdoctoral Fellow, EPFL – École Polytechnique Fédérale de Lausanne – Swiss Federal Institute of Technology in LausanneLicensed as Creative Commons – attribution, no derivatives.