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	<title>The Why Files &#187; Diversity and adaptations of organisms</title>
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		<title>Biology: critters that should not exist!</title>
		<link>http://whyfiles.org/2011/biology-critters-that-should-not-exist/</link>
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		<pubDate>Thu, 29 Dec 2011 17:23:49 +0000</pubDate>
		<dc:creator>svmedaristwf</dc:creator>
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		<category><![CDATA[Structure and function in living systems]]></category>
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		<category><![CDATA[Archaea]]></category>
		<category><![CDATA[bacteria bacteriology]]></category>
		<category><![CDATA[biodiversity]]></category>
		<category><![CDATA[cholera]]></category>
		<category><![CDATA[ecology]]></category>
		<category><![CDATA[evolutionary biology]]></category>
		<category><![CDATA[flashlight squid]]></category>
		<category><![CDATA[hyperthermophile]]></category>
		<category><![CDATA[Margaret McFall-Ngai]]></category>
		<category><![CDATA[meiofauna]]></category>
		<category><![CDATA[Robert Higgins]]></category>
		<category><![CDATA[symbiosis symbiont symbiotic]]></category>
		<category><![CDATA[taxonomy]]></category>
		<category><![CDATA[Thomas Brock]]></category>
		<category><![CDATA[University of Wisconsin Madison UW-Madison]]></category>
		<category><![CDATA[Yellowstone National Park]]></category>

		<guid isPermaLink="false">http://whyfiles.org/?p=21484</guid>
		<description><![CDATA[Lake Vostok could house ancient bacteria, but we already know that bacteria can live in boiling water or light up a glowing squid. Countless weird-and-weirdest critters live between grains of sand... Curious about biology's strange shelf?]]></description>
			<content:encoded><![CDATA[<h3>Critters, critters, everywhere!</h3>
<p>Astronomers have just discovered two Earth-size, rocky planets around a nearby star. Though the planets are way too broilsome for life, they suggest that steady improvements in telescope technology has made the discovery of habitable planets just a matter of time.</p>
<p>
  But as astrobiologists continue to search for life in space, geo-biologists (ok, we coined that) continue to find bizarre life in strange places on Earth: in the dark ocean depths, between grains of sand, and at roasty-toasty temperatures once considered deadly.</p>
<div class="imgBigClear">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/kepler20e.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/kepler20e.jpg" alt="Illustration of brown planet mottled with red in space and sun-like star in the distance" title="Kepler planet" width="620" height="auto" class="alignnone size-full wp-image-21500" /></a></p>
<div class="attrib">Illustration: <a href="http://www.nasa.gov/mission_pages/kepler/news/kepler-20-system.html">NASA/Ames/JPL-Caltech</a></div>
<div class="caption">An artist&#8217;s rendition of one of the rocky planets just discovered by the Kepler mission. It&#8217;s just a bit smaller than Earth &#8212; and a lot hotter, but it still raises questions about the different forms that life could take in space &#8212; and on Earth.</div>
</div>
<h3>Hot, humid, and totally alive!</h3>
<p>
  Fifty years ago, nobody believed organisms could survive near the boiling point of water. When Thomas Brock started probing the hot springs in Yellowstone in the 1960s, he was not looking to overthrow a ground rule of biology. Instead, the University of Wisconsin-Madison professor, then at Indiana University, sought to study bacteria in a simplified, real-world environment.</p>
<div class="imgBigClear">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/yellowstone_bacteria_pool.jpg">
<div class="enlarge">ENLARGE!!</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/yellowstone_bacteria_pool.jpg" alt="Smoldering pool of bright blue water is surrounded by halo of dark orange. Land surrounding pool is purple" title="Yellowstone's Grand Prismatic Spring" width="620" height="auto" class="alignnone size-full wp-image-21496" /></a></p>
<div class="attrib">Photo: <a href="http://commons.wikimedia.org/wiki/File:Grand_prismatic_spring.jpg">Jim Peaco, National Park Service</a></div>
<div class="caption">An aerial view of Grand Prismatic Spring in Yellowstone National Park. Steam rises from hot, sterile water surrounded by mats of brilliant orange algae and bacteria. Yellowstone&#8217;s hot springs and boiling mud pots have been a world headquarters for the discovery of thermophilic (heat-loving) microbes. The spring is approximately 75 by 91 meters.</div>
</div>
<p>  At the time, and even today, precious little was known about how bacteria live their lives &#8212; unless they cause disease.</p>
<p>
  As Brock sampled his way up a hot stream, he approached its source in a hot spring, and the water temperature rose steadily.</p>
<p>
  At the time, biologists thought life would not tolerate temperatures near 80&deg;  C. But Brock kept finding bacteria, so he kept looking. Eventually, he found some that could live and reproduce near the temperature of boiling water &#8212; 100&deg; C.</p>
<p>
  The prize of his collection was a bacterium he named Thermus aquaticus (for its hot-water habitat) and placed in a public repository for study by other scientists.</p>
<div class="box300"><a href="http://whyfiles.org/wp-content/uploads/2011/12/thermophilic_bacteria.jpg">
<div class="enlarge">ENLARGE!!</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/thermophilic_bacteria.jpg" alt="Flat dark orange mass is textured like a sponge" title="Thermophilic bacteria" width="300" height="auto" class="alignnone size-full wp-image-21497" /></a></p>
<div class="attrib">Photo: <a href="http://commons.wikimedia.org/wiki/File:Thermophilic_bacteria.jpg">Amateria1121</a></div>
<div class="caption">Thermophilic bacteria at Mickey Hot Springs, Oregon, gather minerals that eventually turn into solid rock.</div>
</div>
<p>
  Over the years, T. aquaticus proved interesting indeed. For one thing, it was the first of more than 50 species of thermophilic bacteria known to tolerate or require temperatures near water&#8217;s boiling point.</p>
<p>
  For another, it was the first of the Archaea (ancient ones), primitive microorganisms that scientists now regard as a separate and highly primitive kingdom of life.</p>
<h3>Deep roots indeed</h3>
<p>
  Because thermophiles are Archaeans, and prefer the steamy conditions typical of early Earth, many scientists think they may tell us about the origin of life itself.</p>
<p>
  To any basic scientist, those contributions would be enough. But because their enzymes work in high temperatures, where chemical reactions are faster, the thermophiles have proven to be extraordinarily useful.</p>
<p>
  Today, enzymes derived from thermophiles are used to convert millions of pounds of corn (maize) into sugar to sweeten soft drinks.</p>
<div class="box400">
<iframe width="400" height="300" src="http://www.youtube.com/embed/2KoLnIwoZKU" frameborder="0" allowfullscreen alt="One DNA chain splits, then a small piece attaches to each of the two chains and replicates along them, then the chains split again"></iframe></p>
<div class="attrib"><a href="http://youtu.be/2KoLnIwoZKU">DNA Learning Center</a></div>
<div class="caption">How does PCR work?</div>
</div>
<p>
  But more important, at least to scientists who don&#8217;t guzzle fizzy pop at the lab bench, T. aquaticus supplied TAQ polymerase, the essential enzyme for polymerase chain reaction, AKA PCR.</p>
<p>PCR is an artificial technique that does what living critters do every day &#8212; replicate DNA. But PCR is the rocket ship of replication, since it allows you to multiply a piece of DNA a billion times in a few hours. That produces enough DNA to analyze to your heart&#8217;s content &#8212; for genetic engineering, biotechnology and forensic purposes.</p>
<p>
  PCR depends on TAQ polymerase.</p>
<p>
Aware that PCR and soda pop are both billion-dollar industries, corporations and scientists around the world have frantically searched for other thermophiles that may have equally useful enzymes. They&#8217;re looking in odd places &#8212; not just hot springs and volcanoes, but also deep-sea vents, hot petroleum-bearing rock, the outflow of geothermal power plants, and smoldering piles of garbage.</p>
<div class="imgBigClear">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/bobtail2.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/bobtail2.jpg" alt="Two tiny squid crawl on ocean floor. One squid is orange with florescent spots, the other is smaller, white and also has spots" title="Bobtail squid" width="620" height="auto" class="alignnone size-full wp-image-21494" /></a></p>
<div class="attrib"><a href="http://commons.wikimedia.org/wiki/File:Euprymna_scolopes_(Bobtail_squid).jpg">Nick Hobgood</a></div>
<div class="caption">Two bobtail squid showing their signature bacterial glow, and the animal&#8217;s ability to change color.</div>
</div>
<h3>Prowling for glow-in-the-dark squid</h3>
<p> Call me Bob.</p>
<p>
  Short for bobtail squid. (Did I mention that I&#8217;m a 3-4 centimeter cephalopod, formally Euprymna Scolopes?)</p>
<p>
  Anyway, I hang out in shallow waters around Hawaii. Save your crocodile tears &#8212; somebody&#8217;s got to live in the sunny, tropical ocean. Anyway, here&#8217;s my problem: Even though I have 10 tentacles, I don&#8217;t have spines, poisons, or any other decent defense.</p>
<p>
  So I spend my days burrowed in sand at the ocean bottom, trying to keep out of mischief. Still, a fellow&#8217;s got to eat, don&#8217;tcha know, so I cruise at night, looking to grab a bite.</p>
<p>
  Here&#8217;s the snag: All sorts of nocturnal predators seem to have this thing about calamari sushi.</p>
<h3>Light before flashlights</h3>
<p>
  A long time ago, my ancestors evolved a nifty defense against their big teeth: stealth. Even their tiny squid brains figured out that predators could see them from below, as tasty dark blobs against the bright ocean surface.</p>
<p>
  Since this was before flashlights, my relatives had to improvise. So they press-ganged billions of luminescent bacteria into making light for them. The idea was to make us just as bright as the ocean surface &#8212; and hence invisible.</p>
<p>
  At least, this is how my great-aunt Tentacla tells it. To tell the truth, I think it had more to do with the evolutionary advantage of being hard to see.</p>
<p>
  Anyway, my ancestors fed the bacteria, and gave them a home in two specialized light-emitting organs. These &#8220;photophores&#8221; have a reflective membrane to shine all their light down, toward the hungry predators. They use a diaphragm to control brightness, and even have a lens to spread the light.</p>
<p>
  The photophore reminds me of a backwards eye &#8212; one that makes light rather than detects it.</p>
<p>
  My folks even figured out how to switch the bacteria &#8220;on&#8221; when needed.</p>
<p>
  In return, the bacteria got room and board, in the biological deal they call &#8220;symbiosis&#8221; or &#8220;mutualism.&#8221; Sometimes I think people could learn from this cooperative spirit….</p>
<p>
  But that&#8217;s enough thinking for today. My squid brain is squashed.</p>
<p>
  As I burrow into the sand for another daytime nap, permit me to introduce somebody who considers me almost as fascinating as I do.
</p>
<div class="box350">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/squid_confocal2.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/squid_confocal2.jpg" alt="Blue arm-like appendage is attached to a green organ with three egg shaped holes in it" title="Confocal microscop image of Flashlight squid" width="350" height="auto" class="alignnone size-full wp-image-21516" /></a></p>
<div class="attrib">Courtesy <a href="http://www.medmicro.wisc.edu/labs/mcfall-ngai/images.html">Margaret McFall-Ngai</a>, University of Wisconsin-Madison; confocal microscopy by S. Nyholm.</div>
<div class="caption">The flashlight squid uses this blue-stained arm to &#8220;sweep&#8221; bacteria from the water into three intake holes (arrows). Green and blue stains were used to make this confocal microscope image of a cross-section of the squid&#8217;s bacteria-harvesting apparatus.</div>
</div>
<h3>Seriously speaking…</h3>
<p>Margaret McFall-Ngai, a biologist at University of Wisconsin-Madison, says the bobtail squid may pretend it&#8217;s cooperating in a symbiosis with those light-making bacteria, but the reality is more ominous.</p>
<p>
She says there&#8217;s evidence that this may be slavery, not symbiosis, since the squid, &#8220;inhibits the growth of the bacteria to enhance their luminescence.&#8221; The bacteria, Vibrio fischeri, could make a better living drifting in the ocean, or in the gut of another marine animal, McFall-Ngai observes.</p>
<p>
  The concept of bacterial enslavement broadens our perspective on the many possible relationships in the living world.</p>
<p>
  Most people, if they think about bacteria at all, conjure up disease and decay, but people would be dead without bacteria, since the little critters play essential roles in producing vitamins and preventing disease.</p>
<p>
  Since the <a href="http://whyfiles.org/shorties/236gut_flora/">bacteria in our guts</a> vastly outnumber the cells in our bodies, it helps that they&#8217;re helpful!</p>
<p>
  Nevertheless, and for understandable reasons, bacteriologists have traditionally focused on disease-causing organisms, and, for simplicity, on one species at a time. But that skews our view of how bacteria actually live, says McFall-Ngai.</p>
<h3>Three cheers for complexity!</h3>
<p>
  Complexity and subtlety may be the hallmarks of these interactions, and the complexity begins by recognizing that V. fischeri is closely related to V. cholerae, which causes the human intestinal disease, cholera.</p>
<p>
  Cholera is caused by a V. cholera toxin similar to a toxin produced by the light-emitting bacterium. But far from harming the poor little bobtail, that toxin signals it to secrete food for V. fischeri, so the toxin is really a chemical &#8220;dinner bell.&#8221;</p>
<p>
  And this raises the intriguing notion that a cholera bug secretes toxins not to kill its host but to discuss its menu. If so, our whole notion of pathogenesis may need rewriting, McFall-Ngai suggests. &#8220;Maybe when we&#8217;ve been studying cholera pathogenesis we&#8217;ve been studying an aspect of a normal conversation that&#8217;s gone wrong.&#8221;</p>
<p>
  Indeed, the traditional bacteriological view of bacteria as pathogens to be studied in pure culture may be &#8220;like trying to understand the complexity of all the cultures that lived in Paris by studying the activity of the Nazi occupiers,&#8221; McFall-Ngai suggests. &#8220;You are studying groups that don&#8217;t belong there, and have disrupted the normal activities.&#8221;</p>
<p>
  Want more on how the <a href="http://whyfiles.org/2010/sustaining-symbiosis-new-clues/">flashlight squid</a> bullies its bacterial brethren?</p>
<div class="imgBigClear">
<a id="rollover" href="#" title="Meiofauna rollover"></a></p>
<div class="attrib">Both images courtesy <a href="http://www.gastrotricha.unimore.it/picturegallery.htm">M. Antonio Todaro</a></div>
<div class="caption">Meet the meiofauna. The first little guy is from the subgenus Chaetonotus. Rollover to meet Heteroxenotrichula squamosa.</div>
</div>
<h3>Between the grains</h3>
<p>(1996 story, only photos have been updated)</p>
<p>
To zoologist Robert Higgins, small is beautiful. His infatuation with small creatures &#8212; &#8220;meiofauna&#8221; &#8212; dates to a student job in a biology lab that paid 35 cents an hour. Instead of quitting for more lucrative work, Higgins was intrigued.</p>
<p>
  He&#8217;d heard about tiny, amazingly diverse creatures, and put grains of sand and muck through a fine mesh, and used a microscope to find hundreds of organisms.</p>
<p>
  Forty-four years later, Higgins has retired from the Smithsonian Institution, but he&#8217;s still goggling at meiofauna &#8212; a complex group of animals found in most Earthly environments.</p>
<p>
  Indeed, a handful of wet sand could contain more biological diversity than a whole rain forest, Higgins says.</p>
<p>
  In the course of peering through countless microscopes, Higgins has discovered hundreds of species. With Danish biologist Reinhardt Kristensen, he found an entire phylum, called Loricifera.</p>
<p>
  Phyla are the broadest categories of organisms, based on structure, and according to the <a href="http://www.meiofauna.org/">International Association of Meiobenthologists</a>, &#8220;The majority of recognized phyla have meiofaunal representatives. Currently, 20 phyla considered to be meiofaunal from the 34 recognized phyla of the Kingdom Animalia. Out of these 20 phyla, five are exclusively meiofaunal in size.&#8221;</p>
<div class="box350left">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/anhydro.jpg"><img src="http://whyfiles.org/wp-content/uploads/2011/12/anhydro.jpg" alt="Active phase resembles a slug; during anhydrobiosis, it shrinks to a ball about half as large." title="A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis." width="350" height="248" class="alignnone size-full wp-image-21529" /></a></p>
<div class="attrib">Photo: <a href="http://users.unimi.it/ricci/html/anhydro.htm">Giulio Melone</a>, department of biology, Milan University.</div>
<div class="caption">A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis. The dormant, dehydrated bdelloid has greater resistance to environmental stress but is ready to spring back to the active form in conducive conditions.</div>
</div>
<p>
  Meiofauna living between grains of sand have made some fancy adaptations to their harsh environment. Some have hooks on their feet, used to grab the sand. Others have hooked mouthparts, also useful for locomotion.</p>
<h3>Beyond freeze-dried</h3>
<p>
  To survive a difficult environment, meiofauna called tartigrades have evolved an amazing adaptation  called &#8220;anhydrobiosis.&#8221; In this form of suspended animation, the animals replace water in their cell membranes with sugar, protecting the membrane from destruction through radiation and freezing. Microorganisms die when their cell membrane ruptures.</p>
<p>
During anhydrobiosis, organisms are rather like plant seeds or bacterial spores, Higgins explains. &#8220;They can dry up for 100 years, and be rewetted, and come right back to active metabolism.&#8221;</p>
<p>
  Fun is fun. But what is the practical importance of studying stuff that can hardly be seen, doesn&#8217;t seem to cause disease, and is &#8212; at least to some &#8212; utterly ugly?</p>
<p>
  In other word, who cares about microscopic beach crud?</p>
<div class="box200">
<a href="http://whyfiles.org/wp-content/uploads/2011/12/beach2.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/beach2.jpg" alt="Toddler boy in summer outfit and sun hat squats on sand, holding sand toys and peering into a bucket" title="Beachcombing toddler" width="200" height="auto" class="alignnone size-full wp-image-21498" /></a></p>
<div class="attrib">Photo: <a href="http://www.flickr.com/photos/chr1sp/2559825337/">Chris. P</a></div>
<div class="caption">Has this young scientist found some miraculous meiofauna in the blue bucket?</div>
</div>
<h3>Meet the beach-cleaning crew</h3>
<p>
  Anybody who likes to hang on the sand should be interested, Higgins says. &#8220;This is the system that helps keep our beaches clean.&#8221; Plankton, bacteria, all sorts of dead material is continually washing ashore, and a lot of people love to sit on beaches.</p>
<p>
  There&#8217;s a public-health angle here. Hookworms occur on beaches where dogs defecate, but meiofauna may consume hookworms, along with other nematodes. &#8220;So if we upset that, we could upset beach cleanliness,&#8221; Higgins says.</p>
<p>
  Higgins notes that meiofauna comprise a basic part of the food web, and disturbing them could have unforeseen consequences for the entire system.</p>
<p>
  Still, it&#8217;s hard to escape the notion that most of the motivation here is the pure scientific urge to discover, to classify, to understand. Meiofauna, Higgins notes, were seen under the microscope Anton van Leeuwenhoek invented in 1683.</p>
<p>
  The key to finding these things, Higgins indicates, in patience, technology, curiosity &#8212; and institutional support. &#8220;If you stare through a microscope for hour after hour, you have a chance of finding these things, but if you need to get out a certain number of papers each year, you have to take shortcuts and you won&#8217;t find as much.&#8221;</p>
<div class="imgBigClear"><a href="http://whyfiles.org/wp-content/uploads/2011/12/black_smoker1.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/12/black_smoker1.jpg" alt="Mound of sand, covered in white and pink worms, emits three plumes of black water. Two canisters hold instruments." title="Black smoker" width="620" height="auto" class="alignnone size-full wp-image-21502" /></a></p>
<div class="attrib">Photo: <a href="http://www.pmel.noaa.gov/vents/gallery/smoker-images.html">NOAA PMEL Vents Program </a></div>
<div class="caption">At mid-oceanic ridges, scientists have found &#8220;black smokers&#8221;  &#8212; <a href="http://www.pmel.noaa.gov/vents/about.html">vents</a> for geologically heated, chemical-rich groundwater.  The weird organisms at these ridges may thrive in super-hot conditions or live independently of sunlight and photosynthesis. Mid-oceanic ridges even have been the site of the first life.</div>
</div>
<h3>Fantastic freak show</h3>
<div class="bullets">
<ul>
<h3>Biology has lots of other oddities:</h3>
<li> A shrimplike native to Panama&#8217;s Pacific beaches transports itself by rolling. When the animal washes ashore, it arcs its body into a ring and rolls back into the water, pushed by the head and tail at the stately pace of 3.5 centimeters per second. Nannosquilla decernspinosa may have learned to spin in its cramped burrows, but it&#8217;s the only known rolly-roller in the animal kingdom.</li>
<li> Sponges, considered the first multicellular organisms, were always thought to be dumb, simple filter-feeders that strain their dinner from sea water. But now it appears that some sponges in the phylum Cladorhizidae, living in the Mediterranean, are willing to reach out and touch their prey. The sponge has filaments that capture plankton and reel them in for digestion.</li>
<li> Bacteria can live deep underground, and in 2006 a team <a href="http://www.universetoday.com/851/bacteria-found-deep-underground/" > found</a> bacteria 3 kilometers below South Africa, in a niche that had been isolated from the surface for several million years. The discovery demonstrates the resilience of life on Earth and hints that life could exist deep inside Mars.
</li>
<li> A large number of ancient bacterial relatives &#8212; Archaea &#8212; live in the Antarctic. These critters are a large part of the food web in a cold, remote place whose ocean is a major source of protein in our diet.</li>
</ul>
</div>
<div id="writer">
<p>&#8211; David J. Tenenbaum
</p>
</div>
<div class="relateds">
<div style="display: none;">
<a class="simple-footnote" title="Thermophiles like it hot." id="return-note-21484-1" href="#note-21484-1"><sup>1</sup></a><br />
<a class="simple-footnote" title="Thermophiles in Yellowstone." id="return-note-21484-2" href="#note-21484-2"><sup>2</sup></a><br />
<a class="simple-footnote" title="More about squid-vibrio symbiosis." id="return-note-21484-3" href="#note-21484-3"><sup>3</sup></a><br />
<a class="simple-footnote" title="More about Vibrio fishereri." id="return-note-21484-4" href="#note-21484-4"><sup>4</sup></a><br />
<a class="simple-footnote" title="Life in the vents multimedia." id="return-note-21484-5" href="#note-21484-5"><sup>5</sup></a><br />
<a class="simple-footnote" title="Meiofauna picture gallery." id="return-note-21484-6" href="#note-21484-6"><sup>6</sup></a><br />
<a class="simple-footnote" title="More meiofauna resources." id="return-note-21484-7" href="#note-21484-7"><sup>7</sup></a><br />
<a class="simple-footnote" title="Make your own PCR reaction." id="return-note-21484-8" href="#note-21484-8"><sup>8</sup></a><br />
<a class="simple-footnote" title="Video: watch a water bear go into anhydrobiosis." id="return-note-21484-9" href="#note-21484-9"><sup>9</sup></a><br />
<a class="simple-footnote" title="Anhydrobiosis and radiation resistance." id="return-note-21484-10" href="#note-21484-10"><sup>10</sup></a><br />
<a class="simple-footnote" title="Meiofauna classroom activity." id="return-note-21484-11" href="#note-21484-11"><sup>11</sup></a><br />
<a class="simple-footnote" title="More strange biology." id="return-note-21484-12" href="#note-21484-12"><sup>12</sup></a>
</div>
</div>
<div id="relateds"><h3>Terry Devitt, editor; S.V. Medaris, designer/illustrator; David J. Tenenbaum, feature writer; Amy Toburen, content development executive; Molly Simis, project assistant</h3></div>
<div class="simple-footnotes"><h3>Bibliography</h3><ol><li id="note-21484-1"><a href="http://serc.carleton.edu/microbelife/extreme/extremeheat/">Thermophiles</a> like it hot. <a href="#return-note-21484-1">&#8617;</a></li><li id="note-21484-2"><a href="http://serc.carleton.edu/microbelife/extreme/extremeheat/yellowstone.html">Thermophiles</a> in Yellowstone. <a href="#return-note-21484-2">&#8617;</a></li><li id="note-21484-3">More about <a href="http://serc.carleton.edu/microbelife/topics/marinesymbiosis/squid-vibrio/collection.html">squid-vibrio</a> symbiosis. <a href="#return-note-21484-3">&#8617;</a></li><li id="note-21484-4">More about <a href="http://microbewiki.kenyon.edu/index.php/Vibrio_fischeri_NEU2011">Vibrio fishereri</a>. <a href="#return-note-21484-4">&#8617;</a></li><li id="note-21484-5"><a href="http://www.pmel.noaa.gov/vents/multimedia.html">Life in the vents</a> multimedia. <a href="#return-note-21484-5">&#8617;</a></li><li id="note-21484-6"><a href="http://www.gastrotricha.unimore.it/picturegallery.htm">Meiofauna</a> picture gallery. <a href="#return-note-21484-6">&#8617;</a></li><li id="note-21484-7">More meiofauna <a href="http://www.meiofauna.org/relatwww.html">resources</a>. <a href="#return-note-21484-7">&#8617;</a></li><li id="note-21484-8">Make your own <a href="http://learn.genetics.utah.edu/content/labs/pcr/">PCR reaction</a>. <a href="#return-note-21484-8">&#8617;</a></li><li id="note-21484-9"><a href="http://www.youtube.com/watch?v=B14MXZurTXA">Video</a>: watch a water bear go into anhydrobiosis. <a href="#return-note-21484-9">&#8617;</a></li><li id="note-21484-10">Anhydrobiosis and <a href="http://blogs.discovermagazine.com/notrocketscience/tag/anhydrobiosis/">radiation resistance</a>. <a href="#return-note-21484-10">&#8617;</a></li><li id="note-21484-11">Meiofauna <a href="http://serc.carleton.edu/resources/17142.html">classroom activity</a>. <a href="#return-note-21484-11">&#8617;</a></li><li id="note-21484-12">More <a href="http://biologybiozine.com/categories/strange_biology/">strange biology</a>. <a href="#return-note-21484-12">&#8617;</a></li></ol></div>]]></content:encoded>
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		<title>A Story of the Bacterium and the Fly</title>
		<link>http://whyfiles.org/2011/a-story-of-the-bacterium-and-the-fly/</link>
		<comments>http://whyfiles.org/2011/a-story-of-the-bacterium-and-the-fly/#comments</comments>
		<pubDate>Thu, 20 Oct 2011 18:20:52 +0000</pubDate>
		<dc:creator>svmedaristwf</dc:creator>
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		<guid isPermaLink="false">http://whyfiles.org/?p=19689</guid>
		<description><![CDATA[Bacteria can help or harm their hosts. Now we hear how one genus of bacteria can multiply fly reproduction. In this symbiosis, both parties benefit. This bacterium also alters insect immunity, and could lead to new tactics for killing horrific parasites. ]]></description>
			<content:encoded><![CDATA[<h3>Your cell = my home?</h3>
<p>
  Poke deep inside an insect cell, and you may be in for a shock. At least we were startled to learn that bacteria live inside many insects, including the fruit fly, one of the workhorses of biology.</p>
<div class="box150"><a href="http://whyfiles.org/wp-content/uploads/2011/10/mauritiana.gif"><img src="http://whyfiles.org/wp-content/uploads/2011/10/mauritiana.gif" alt="Dead fruit fly with translucent brown body and big orange eye" title="Drosophila mauritiana" width="150" height="80" class="alignnone size-full wp-image-19714" /></a></p>
<div class="attrib">Photo: <a href="http://www.boldsystems.org/views/taxbrowser.php?taxid=29696">Biodiversity Institute of Ontario</a></div>
<div class="caption">The star of the study, <em>Drosophila mauritiana</em>.</div>
</div>
<p>
  Today, we hear how bacteria of the genus <i>Wolbachia</i> boost egg production in certain fruit flies. The mechanism, says Horacio Frydman, an assistant professor of biology at Boston University, involves a two-step: first the fly makes more egg cells, and then it blocks a process that would normally prune away extra eggs.</p>
<p>
  Insects, like other animals, are frequently &#8220;married&#8221; to bacteria in a relationship that benefits one or both parties. This is common: Bacteria in the cow&#8217;s rumen break down cellulose eaten by the cow. Bacteria in the human gut form vitamin K, necessary for blood clotting.</p>
<p>
  And bacteria in aphids synthesize essential amino acids that the aphids cannot make by themselves.<br />
  <em>Wolbachia</em> are not essential to the fruit flies, but their presence can quadruple egg production.</p>
<div class="imgBigClear">
<h3>Egg development in the fruit fly <em>Drosophila mauritiana</em></h3>
<p><a href="http://whyfiles.org/wp-content/uploads/2011/10/fast3labelled.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/10/fast3labelled.jpg" alt="Series of amoeba-like sacks contain blue circles, speckled with green" title="Laser scanning confocal microscope shows eggs originating in germline stem cell niche. As the eggs mature, they move in egg chambers away from the niche. Wolbachia cells, stained green, congregate in the germline stem cell niche. Germline cells are red; DNA is blue." width="620" height="631" class="alignnone size-full wp-image-19697" /></a></p>
<div class="attrib">Original image courtesy Eva M. Fast and Horacio M. Frydman, Boston University</div>
<div class="caption">Laser scanning confocal microscope shows eggs originating in germline stem cell niche. As the eggs mature, they move in egg chambers away from the niche. Wolbachia cells, stained green, congregate in the germline stem cell niche. Germline cells are red; DNA is blue.</div>
</div>
<h3>Speeding breeding</h3>
<p>
  Producing four times as many offspring &#8220;is a powerful driver of infection,&#8221; Frydman says. “<i>Wolbachia</i> manipulate their host reproduction to favor their own spread in nature,” noting that in less than 20 years after <em>Wolbachia</em> was detected in fruit flies in southern California, the infection had spread as far as Canada. &#8220;It&#8217;s considered  one of the largest pandemics in the recent evolution of life. Because <em>Wolbachia</em> influence their host reproduction, they also impact the evolutionary history of innumerable hosts.&#8221;</p>
<p>
  <em>Wolbachia</em> have been linked with a <a href="http://en.wikipedia.org/wiki/Wolbachia">wide variety of effects</a> in the insect realm. <em>Wolbachia</em> &#8220;lives in at least 20 percent of the world&#8217;s arthropods, including insects, spiders, mites, and crustaceans,&#8221; according to the <a href="http://discover.mbl.edu/intro.htm">Wolbachia project</a>, making them an active area of investigation.</p>
<p>
How could this symbiosis work to increase the number of offspring?
</p>
<p>
  Using sophisticated microscopy, Frydman, Ph.D. student Eva Fast and colleagues tracked the location of <em>Wolbachia</em> in fruit flies. In <em>D. mauritiana</em>, a species native to the Mauritius Islands in the Indian Ocean, the bacteria congregate in the germline stem cell niche &#8212; a structure that supports stem cells that develop into eggs. In <em>D. melanogaster</em>, the bacteria accumulate in the niche that harbors a different type of stem cell, which produces the eggshell. </p>
<p>In the germline stem cell niche, the bacteria actually outnumber mitochondria, organelles involved in making energy for the fly. </p>
<p><div class="box300left">
<a href="http://whyfiles.org/wp-content/uploads/2011/10/melanogaster2.jpg">
<div class="enlarge">ENLARGE</div>
<p><img src="http://whyfiles.org/wp-content/uploads/2011/10/melanogaster2.jpg" alt="Yellow-orange fruit fly with big orange eyes, on bright green leaf" title="Drosophila melanogaster" width="300" height="211" class="alignnone size-full wp-image-19720" /></a></p>
<div class="attrib">Photo: <a href="http://commons.wikimedia.org/wiki/File:Vinegar_fly.jpg">Fir0002/Flagstaffotos</a>, <a href="http://en.wikipedia.org/wiki/GNU_Free_Documentation_License">GFDL</a></div>
<div class="caption">The fruit fly <em>Drosophila melanogaster</em>, a workhorse of bio labs, is a cousin of <em>D. mauritiana</em>, which gets a reproductive supercharge from Wolbachia infection.</div>
</div>
<p>
  Having the bacteria in the germline stem cell niche doubled the rate of division among those stem cells. Further investigation showed that the bacteria later also halved the rate of programmed cell death.<br />
  So the bottom line was a four-fold increase in egg production.</p>
<h3>The virtue of pruning</h3>
<p>
  &#8220;It&#8217;s remarkable that there are two mechanisms being manipulated by the bacteria, the rate of egg production and the rate of programmed cell death,&#8221; says Frydman.</p>
<p>
 Hitting both systems makes sense, Frydman adds, although the mechanisms remain unclear. &#8220;It is not surprising that Wolbachia would evolve to manipulate those two process, because they are key in controlling the rate of egg production, and therefore it has a profound impact in the reproductive success of the infected host and in spreading of bacteria in nature.&#8221;</p>
<p>
    Anything that increases the number of eggs and offspring is likely to be favored by natural selection, Frydman adds.</p>
<div class="box150">
<a href="http://whyfiles.org/wp-content/uploads/2011/10/elephantiasis.jpg"><img src="http://whyfiles.org/wp-content/uploads/2011/10/elephantiasis.jpg" alt="Man sits in chair with only his lower half visible. Both legs and feet are severely swollen." title="Elephantiasis-afflicted man" width="150" height="150" class="alignnone size-full wp-image-19725" /></a></p>
<div class="attrib">Photo: <a href="http://commons.wikimedia.org/wiki/File:Elephantiasis.jpg">CDC</a>, #373</div>
<div class="caption">Parasitic worms cause elephantiasis, which afflicts this man from the Philippines. Could killing <em>Wolbachia</em> prevent this disfiguring disease?</div>
</div>
<p><h3>A healthy thing?</h3>
<p>
    Beyond an insight into the fascinating biology of symbiosis, the finding could also have health implications. Parasitic worms that cause diseases like elephantiasis seem to benefit from <em>Wolbachia</em> infection. </p>
<p>
And <em>Wolbachia</em> can affect insect immunity: Tests have shown that infected fruit flies are more resistant to some viruses, for example. And a recent paper in Nature found that mosquitoes in Australia could not transmit dengue fever if they carried a <em>Wolbachia</em> strain derived from <em>Drosophila</em>.</p>
<p>
    Mosquitoes also transmit malaria. Conceivably, better knowledge of the interaction between <em>Wolbachia</em> and insects might convert mosquitoes from a carrier of this ancient scourge into a defense against it.</p>
<p><p id="date">&#8211; David J. Tenenbaum</p>
<div class="relateds">
<div style="display: none;">
<a class="simple-footnote" title="Wolbachia Enhance Drosophila Stem Cell Proliferation and Target the Germline Stem Cell Niche, Eva M. Fast et al, www.sciencexpress.org / 20 October 2011 / Page 1 / 10.1126/science.1209609" id="return-note-19689-1" href="#note-19689-1"><sup>1</sup></a><br />
<a class="simple-footnote" title="Horacio Frydman." id="return-note-19689-2" href="#note-19689-2"><sup>2</sup></a><br />
<a class="simple-footnote" title="Wolbachia biology." id="return-note-19689-3" href="#note-19689-3"><sup>3</sup></a><br />
<a class="simple-footnote" title="A tale of sex and survival." id="return-note-19689-4" href="#note-19689-4"><sup>4</sup></a><br />
<a class="simple-footnote" title="Wolbachia research database." id="return-note-19689-5" href="#note-19689-5"><sup>5</sup></a><br />
<a class="simple-footnote" title="Wolbachia teaching resources." id="return-note-19689-6" href="#note-19689-6"><sup>6</sup></a><br />
<a class="simple-footnote" title="Controlling dengue fever." id="return-note-19689-7" href="#note-19689-7"><sup>7</sup></a><br />
<a class="simple-footnote" title="Malaria prevention?" id="return-note-19689-8" href="#note-19689-8"><sup>8</sup></a><br />
<a class="simple-footnote" title="Wolbachia makes widows." id="return-note-19689-9" href="#note-19689-9"><sup>9</sup></a><br />
<a class="simple-footnote" title="It even creates new species!" id="return-note-19689-10" href="#note-19689-10"><sup>10</sup></a><br />
<a class="simple-footnote" title="River blindness culprit." id="return-note-19689-11" href="#note-19689-11"><sup>11</sup></a><br />
<a class="simple-footnote" title="Can I borrow your genes?" id="return-note-19689-12" href="#note-19689-12"><sup>12</sup></a>
</div>
</div>
<div id="relateds"><h3>Terry Devitt, editor; S.V. Medaris, designer/illustrator; David J. Tenenbaum, feature writer; Amy Toburen, content development executive; Molly Simis, project assistant</h3></div>
<div class="simple-footnotes"><h3>Bibliography</h3><ol><li id="note-19689-1">Wolbachia Enhance Drosophila Stem Cell Proliferation and Target the Germline Stem Cell Niche, Eva M. Fast et al, www.sciencexpress.org / 20 October 2011 / Page 1 / 10.1126/science.1209609 <a href="#return-note-19689-1">&#8617;</a></li><li id="note-19689-2"><a href="http://www.bu.edu/biology/people/faculty/frydman/">Horacio Frydman</a>. <a href="#return-note-19689-2">&#8617;</a></li><li id="note-19689-3">Wolbachia <a href="http://serc.carleton.edu/microbelife/k12/microbes_within/resources.html">biology</a>. <a href="#return-note-19689-3">&#8617;</a></li><li id="note-19689-4"><a href="http://carlzimmer.com/articles/2001.php?subaction=showfull&#038;id=1177558753&#038;archive=&#038;start_from=&#038;ucat=4&#038;">A tale</a> of sex and survival. <a href="#return-note-19689-4">&#8617;</a></li><li id="note-19689-5">Wolbachia <a href="http://www.wolbachia.sols.uq.edu.au/index.html">research database</a>. <a href="#return-note-19689-5">&#8617;</a></li><li id="note-19689-6">Wolbachia <a href="http://discover.mbl.edu/index.html">teaching resources</a>. <a href="#return-note-19689-6">&#8617;</a></li><li id="note-19689-7">Controlling <a href="http://www.nature.com/news/2011/240811/full/news.2011.503.html">dengue fever</a>. <a href="#return-note-19689-7">&#8617;</a></li><li id="note-19689-8"><a href="http://www.sciencedaily.com/releases/2011/05/110519172915.htm?utm_source=feedburner&#038;utm_medium=feed&#038;utm_campaign=Feed:+sciencedaily+(ScienceDaily:+Latest+Science+News)">Malaria prevention</a>? <a href="#return-note-19689-8">&#8617;</a></li><li id="note-19689-9">Wolbachia <a href="http://www.nature.com/news/1998/990429/full/news990429-8.html">makes widows</a>. <a href="#return-note-19689-9">&#8617;</a></li><li id="note-19689-10">It even creates <a href="http://www.scientificamerican.com/article.cfm?id=bacteria-spurs-speciation">new species</a>! <a href="#return-note-19689-10">&#8617;</a></li><li id="note-19689-11"><a href="http://www.sciencemag.org/content/295/5561/1809.full">River blindness culprit</a>. <a href="#return-note-19689-11">&#8617;</a></li><li id="note-19689-12">Can I borrow <a href="http://www.rochester.edu/news/show.php?id=2963">your genes</a>? <a href="#return-note-19689-12">&#8617;</a></li></ol></div>]]></content:encoded>
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		<title>Methane on the menu in the Gulf of Mexico?</title>
		<link>http://whyfiles.org/2011/methane-on-the-menu-in-the-gulf-of-mexico/</link>
		<comments>http://whyfiles.org/2011/methane-on-the-menu-in-the-gulf-of-mexico/#comments</comments>
		<pubDate>Thu, 06 Jan 2011 20:03:41 +0000</pubDate>
		<dc:creator>admin</dc:creator>
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		<category><![CDATA[British Petroleum BP]]></category>
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		<category><![CDATA[microbe microbiology]]></category>

		<guid isPermaLink="false">http://whyfiles.org/?p=13193</guid>
		<description><![CDATA[The BP spill released about 160,000 tons of methane into the Gulf of Mexico, but a new study shows that it was eaten by friendly bacteria. The seabed contains an astonishing amount of methane, a strong greenhouse gas. So can bacteria reduce the global warming hazard of massive methane releases?]]></description>
			<content:encoded><![CDATA[<h3>Incredible disappearing methane</h3>
<p>When Deepwater Horizon blew up and melted down in April, the wound it tore in the Earth&#8217;s crust released a gusher of crude oil, estimated at 4.2 million barrels, into the Gulf of Mexico.</p>
<h2 class="pullquote">The massive microbial munching of methane during the BP spill may be the only good news from the Deepwater Horizon disaster.</h2>
<p>The blowout also released about 160,000 tons of methane. If you counted molecules in BP&#8217;s blowout, methane (CH<sub>4</sub>), the simple hydrocarbon that fuels stoves, furnaces and electric generators, was the single most abundant one.</p>
<p>But a report published in today&#8217;s Science shows that BP&#8217;s methane was totally devoured by microbes in the Gulf of Mexico, leaving less than .01 percent of the methane to enter the atmosphere. &#8220;We measured the sea-to-air flux of methane and found it was completely negligible,&#8221; says first author John Kessler, an assistant professor of oceanography at Texas A&#038;M University.</p>
<p>Within four months of the April 20, 2010, blowout, a population explosion among methane-eating bacteria native to the Gulf decomposed virtually all of the methane, mainly in deep water, says Kessler.</p>
<div id="attachment_13242" class="wp-caption alignright" style="width: 356px"><a href="http://whyfiles.org/wp-content/uploads/2011/01/1CTD_sampling.jpg"><img class="size-full wp-image-13242" title="Study author John Kessler extracts a water sample from a device that detects changes in water conductivity and temperature with depth." src="http://whyfiles.org/wp-content/uploads/2011/01/1CTD_sampling.jpg" alt="On a ship, man looking at tube attached to tank valve, man behind him bent over checking tubes" width="346" height="520" /></a><p class="wp-caption-text">Study author John Kessler extracts a water sample from a device that detects changes in water conductivity and temperature with depth.<br /><a href='http://www.noaa.gov/deepwaterhorizon/video/oceanservice/deepwaterhorizon/images.html#146'>NOAA</a> Pisces.</p></div>
<p>The study offered three lines of evidence that bacteria were &#8220;eating&#8221; the released methane:<br />
<strong>
<ul>
<li type="disc">Methane levels in the Gulf fell up to 10,000 times between June and October.</li>
<li type="disc">Methane-munching microorganisms became extremely abundant downstream of the blowout. &#8220;Over the summer, the methane degraders were higher than we have ever seen at any other place in the world,&#8221; says Kessler.</li>
<li type="disc">Dissolved oxygen in the water dropped as methane and oxygen reacted to form carbon dioxide and water, Kessler says. &#8220;Once we summed up all the lost oxygen in the area of the methane plume, we saw that it could only be explained by a complete [microbial] consumption of this methane.&#8221;</li>
</ul>
<p></strong><br />
Although oxygen depletion is already a concern in the Gulf&#8217;s &#8220;<a href="http://whyfiles.org/282dead_zone/">Dead Zone</a>,&#8221; the average loss was only 3 percent, Kessler says.</p>
<p>In a previous study, ethane and propane, two other natural gases that BP also released, decomposed even faster than methane, and were no higher than background levels by early fall. In both studies, Kessler collaborated with David Valentine of the University of California at Santa Barbara.</p>
<h3>Cool news for your atmosphere</h3>
<p>In the short term, spilled methane is less environmentally dangerous than crude oil, but it can pose a global warming problem in the long term, since a molecule of methane stores much more heat than a molecule of carbon dioxide.<br />
Methane seeps are frequently found at ocean floors, where methane from decomposition enters the ocean. And unfathomable quantities of <a href="http://whyfiles.org/119nat_gas/">frozen methane</a> are stored beneath  the seabed.</p>
<p>So inquiring minds want to know: If and when this methane enters the ocean, could it reach the atmosphere and accelerate global warming?</p>
<div id="attachment_13200" class="wp-caption aligncenter" style="width: 423px"><a href="http://whyfiles.org/wp-content/uploads/2011/01/1kessler1HR.jpg"><img class="size-full wp-image-13200  " title="Pisces, a research ship of the National Oceanic and Atmospheric Administration, was a floating laboratory to study Deepwater Horizon's aftershocks. Photo: John D. Kessler/TAMU" src="http://whyfiles.org/wp-content/uploads/2011/01/1kessler1HR.jpg" alt="Large multi-level ship, top festooned with scientific instruments, at dock; with a smaller boat docked alongside." width="413" height="309" /></a><p class="wp-caption-text">Pisces, a research ship of the National Oceanic and Atmospheric Administration, was a floating laboratory to study Deepwater Horizon&#39;s aftershocks.<br /> Photo: John D. Kessler/TAMU</p></div>
<p>The giant Deepwater spill contained too little methane to affect atmospheric levels, says Kessler, &#8220;but it does simulate a very energetic release from a seep or a methane hydrate, and so we were interested in using it as an analog for understanding how a massive submarine release of methane might behave.&#8221;</p>
<p>Although the microbes-eat-methane story provides a rare bright spot in BP&#8217;s ecological disaster, it&#8217;s not clear what would happen in shallow water, and in places lacking natural methane and a ready supply of methane eaters.</p>
<p>&#8220;The Gulf of Mexico has many natural methane seeps,&#8221; says Kessler, &#8220;that probably account for why Gulf waters are populated with these microorganisms, which are ready to degrade methane once there is a massive restocking of their &#8216;buffet.&#8217; How this may play out at another place, without the natural seeps, I&#8217;m not sure.&#8221;</p>
<p>Within four months, bacteria had spawned enough offspring to devour essentially all of the added methane in the Gulf. &#8220;But if the bacteria are at lower abundance, would this take five months or two years? We don&#8217;t know.&#8221;</p>
<p id="date">&#8211; David J. Tenenbaum</p>
<div class="relateds">
<div style="display: none;"><a class="simple-footnote" title="A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico, J.D. Kessler et al, Science, 7 Jan. 2011." id="return-note-13193-1" href="#note-13193-1"><sup>1</sup></a></div>
</div>
<div id="relateds"><h3>Terry Devitt, editor; S.V. Medaris, designer/illustrator; David J. Tenenbaum, feature writer; Amy Toburen, content development executive; Molly Simis, project assistant</h3></div>
<div class="simple-footnotes"><h3>Bibliography</h3><ol><li id="note-13193-1">A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico, J.D. Kessler et al, Science, 7 Jan. 2011. <a href="#return-note-13193-1">&#8617;</a></li></ol></div>]]></content:encoded>
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		<title>Biofuel advance</title>
		<link>http://whyfiles.org/2010/biofuel-advance/</link>
		<comments>http://whyfiles.org/2010/biofuel-advance/#comments</comments>
		<pubDate>Fri, 10 Sep 2010 12:29:31 +0000</pubDate>
		<dc:creator>svmedaristwf</dc:creator>
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		<guid isPermaLink="false">http://whyfiles.org/?p=9391</guid>
		<description><![CDATA[Ethanol in gasoline now comes mainly from corn, a food crop. Cellulose, found in crop wastes, wood and switchgrass, could be a great source of ethanol, if only the yeast that makes ethanol could digest cellulose. A new genetic alteration forced yeast to break down cellulose, and then convert it into ethanol.]]></description>
			<content:encoded><![CDATA[<div class="box200"><a rel="attachment wp-att-9476" href="http://whyfiles.org/2010/biofuel-advance/gas_pump_sm/"><img class="alignnone size-full wp-image-9476" title="gas_pump_sm" src="http://whyfiles.org/wp-content/uploads/2010/09/gas_pump_sm1.jpg" alt=" Close-up of gas pumps with 'Contains 10% ethanol' sticker" width="180" height="287" /></a></div>
<h3>From French bread to non-fossil fuel?</h3>
<p>Yeast can ferment corn starch into ethanol to be added to gasoline, but that diverts millions of tons of food from hungry people.  Researchers are trying to ferment many other plant carbohydrates, especially cellulose, the tough chain-like molecule that stiffens the cell wall so plants can stand by themselves.</p>
<div class="caption">Gasoline already contains corn-ethanol; a new study shows a new way to make ethanol from switchgrass or waste wood.</div>
<div class="attrib">Photo: David J. Tenenbaum</div>
<p>Unfortunately, the yeasts used to make ethanol have no taste for cellulose.</p>
<p>In this week&#8217;s Science, Jamie Cate, in the department of molecular and cell biology at the University of California at Berkeley, reports a transfer of two genes from a fungus to ethanol-making yeast. Although the fungus was discovered on French bread in the 1840s, the result was not exactly a fine Burgundy, or even a gallon of cheap jug wine, but it was a proof of principle that a single organism could, almost single-yeastedly, convert cellulose into ethanol.</p>
<p>Mon dieu!</p>
<p>The advance may hasten the day when waste wood, crop residues and fast-growing crops such as switchgrass can replace edible crops like corn and sugar cane in producing fuel.</p>
<div class="imgBigClear">
<p><a href="http://whyfiles.org/wp-content/uploads/2010/09/wastewood.jpg"><img class="alignnone size-full wp-image-9414" title="wastewood" src="http://whyfiles.org/wp-content/uploads/2010/09/wastewood.jpg" alt="" width="620" height="465" /></a></p>
<div class="attrib">Photo:  <a href="http://commons.wikimedia.org/wiki/File:Waste_wood_1.JPG">Tetris L</a></div>
<div class="caption">Woody biomass or wood waste could be made into biofuel for cars, trucks or airplanes.</div>
</div>
<div class="box350">
<p><a href="http://whyfiles.org/wp-content/uploads/2010/09/biofuel_conv_diagr.jpg"><img title="biofuel_conv_diagr" src="http://whyfiles.org/wp-content/uploads/2010/09/biofuel_conv_diagr.jpg" alt="Colorful diagram of the production and consumption cycle of biofuels" width="350" height="402" /></a></p>
<div class="attrib">Graphic: <a href="http://www.jgi.doe.gov/education/bioenergy/bioenergy_1.html">US DOE</a></div>
<div class="caption">If biofuels can be made from plant material, the net global warming impact should be zero, since growing plants absorb carbon dioxide from the atmosphere.</div>
</div>
<h3>Raise a glass to success!</h3>
<p>&#8220;It&#8217;s a proof of principle using lab strains,&#8221; says Cate.</p>
<p>The genetic transfer enabled a single strain of yeast to convert cellulose in plant cell walls into ethanol. After commercial enzymes busted the cellulose into short chains of glucose units, the yeast:</p>
<div class="bullets">
<p><img src="http://whyfiles.org/wp-content/uploads/2010/09/bullet1.gif" alt="" width="25" height="26" />Transported those chains inside the yeast cell,</p>
<p><img src="http://whyfiles.org/wp-content/uploads/2010/09/bullet1.gif" alt="" width="25" height="26" />Converted the chains into individual  glucose molecules, and</p>
<p><img src="http://whyfiles.org/wp-content/uploads/2010/09/bullet1.gif" alt="" width="25" height="26" /> Fermented that glucose to ethanol (which is what the yeast does naturally).</p>
</div>
<p>The short chains of glucose that the <em> Neurospora crassa</em> fungus extracts from cellulose do not normally enter the yeast cell, but the transporters ensure that they will enter the transformed yeast, enabling the yeast to make ethanol from normally indigestible compounds.</p>
<h3>Taking lessons from fungi</h3>
<p>The research began with a basic question. A large portion of plant biomass is cellulose, and &#8220;microorganisms in the wild live on plants; they obviously have  figured out how to degrade plants as food,&#8221; says Cate.  &#8220;Plants have been figuring out ways to prevent microbes from doing this, so there&#8217;s this ongoing battle, and we knew some fungi would be very good at decomposing cellulose.&#8221;</p>
<p>Cate focused on <em>N. crassa</em>, a well-studied fungus that lives in burned-over areas, but also has a taste for a stale baguette. The research team moved two genes from the fungus into <em>Saccharomyces cerevisiae</em>, a yeast widely used to ferment sugar into ethanol.</p>
<p>One gene forms structures in the yeast&#8217;s cell wall that draw short chains of glucose into the cell.  The second gene makes beta-glucosidase, an enzyme that the fungus (and now the yeast) use inside the cell to snip the short chains of glucose into individual glucose molecules, where the yeast converts them into ethanol.</p>
<div class="imgBigClear">
<p><a rel="attachment wp-att-9413" href="http://whyfiles.org/2010/biofuel-advance/switchgrass_closeup/"><img class="alignnone size-full wp-image-9413" title="switchgrass_closeup" src="http://whyfiles.org/wp-content/uploads/2010/09/switchgrass_closeup.jpg" alt="Field of tall green grass growing in bunches, some exposed dried earth in the very foreground" width="620" height="643" /></a></p>
<div class="attrib">Photo:  <a href="http://www.ars.usda.gov/is/graphics/photos/sep07/d854-1.htm">Stephen Ausmus/USDA</a></div>
<div class="caption">Switchgrass has less environmental impact than corn, and so may be a better source of ethanol. But switchgrass plantations could still divert land needed to grow food.</div>
</div>
<h3>Raise a glass to success!</h3>
<p>Although the short chains of glucose that the fungus extracts from cellulose is not digestible to normal yeast, the transformed yeast used these short chains to produce an abundance of ethanol.  &#8220;It&#8217;s a proof of principle using lab strains,&#8221; says Cate. &#8220;We in the Energy Bioscience Institute [a collaboration of  UC-Berkeley, the University of Illinois, Lawrence Berkeley Laboratory and BP] have colleagues who are helping us look at some really robust, industrial yeasts to see how the transporters work in those systems.&#8221;</p>
<div class="box300">
<p><a rel="attachment wp-att-9411" href="http://whyfiles.org/2010/biofuel-advance/galazaka2hr/"><img class="alignnone size-full wp-image-9411" title="galazaka2hr" src="http://whyfiles.org/wp-content/uploads/2010/09/galazaka2hr.jpg" alt="One pair and trio of bright green circles with smaller circle inside against black backdrop" width="300" height="505" /></a></p>
</div>
<p>Cate says transporters are key. &#8220;Any cell is a fortress, with a membrane  or a cell wall that keeps things out to protect its innards. To get a small molecule in or out, there has to be a way, and these are the transporters, which live in the cell membrane, with parts on the outside and parts on the inside.&#8221;</p>
<p>The study was &#8220;a pretty slick example of how genomic technology can rapidly get you to the gene you care about,&#8221; says Steven Slater, associate director of the <a href="http://www.glbrc.org/">Great Lakes Bioenergy Research Center</a>. &#8220;They used a combination of published literature on genes that are differentially expressed when several fungi are exposed to cellulose, and were able to rapidly go from there down to something that looks like transporter.&#8221;</p>
<div class="attrib">Image: ©Science/AAAS</div>
<div class="caption">Cellulose-eating yeast cells after transformation: The green marks the transporter structures made by genes moved from a cellulose-eating fungus.</div>
<h3>Training a workhorse</h3>
<p>The key, Slater says, is that &#8220;they took a workhorse organism that is primarily used for the production of ethanol and gave it a new genetic tool that could be used to get things other than glucose inside the cell; that&#8217;s important for producing ethanol from cellulosic biomass.&#8221;</p>
<p>Indeed, Cate says, many organisms have ways to transport fragments of cellulose: &#8220;You can find these all over in nature, including in the black truffle, a fungal delicacy that grows symbiotically on oak trees.&#8221;</p>
<p>Cate expects further progress. &#8220;We in the Energy Bioscience Institute [a collaboration of  UC-Berkeley, the University of Illinois, Lawrence Berkeley Laboratory and BP] are testing some really robust, industrial yeasts.&#8221;</p>
<p>This process may not be limited to ethanol, Cate says. &#8220;It&#8217;s modular, and it may benefit research groups that have been working on yeast to make all sorts of interesting biofuels: alcohols, or things like diesel or jet fuel.&#8221;</p>
<p>David J. Tenenbaum</p>
<div id="relateds">
<h3>Related Why Files</h3>
<p><a href="http://whyfiles.org/253ethanol/">Motoring on moonshine</a>.</p>
<p><a href="http://whyfiles.org/161renew_en/">News on renewables</a>.</p>
<p>Harvesting <a href="http://whyfiles.org/shorties/204bact_energy"></a>bacteria’s energy.</p>
<p><a href="http://whyfiles.org/shorties/275coffee_diesel/">Coffee:</a> a new biodiesel frontier?</p>
<h3>Bibliography</h3>
<p><a href="http://en.wikipedia.org/wiki/Biofuel">Biofuels</a>.</p>
<p><a href=" http://www.nrel.gov/learning/re_biomass.html">Biomass energy basics</a>.</p>
<p><a href="http://www1.eere.energy.gov/biomass/abcs_biofuels.html">ABCs of biofuels</a>.</p>
<p><a href=" http://en.wikipedia.org/wiki/Cellulosic_ethanol">Cellulosic ethanol</a>.</p>
<p><a href="http://en.wikipedia.org/wiki/Ethanol_fermentation">Ethanol fermentation</a>.</p>
<p>U.S. biofuels <a href="http://www.nature.com/nature/journal/v444/n7120/full/444673a.html">a field in ferment</a>.</p>
<p>U.S. DOE: <a href="http://genomicscience.energy.gov/biofuels/b2bworkshop.shtml">Biomass to biofuels</a>.</p>
<p><a href="http://www.worldwatch.org/taxonomy/term/445">Biofuels for transport</a>.</p>
<p><a href="http://news.discovery.com/tech/cellulosic-ethanol-dealt-a-blow.html">The downside</a>?</p>
<p><a href="http://www.nytimes.com/cwire/2010/02/16/16climatewire-economics-improve-for-first-commercial-cellu-93478.html">Economics improve</a> for cellulosic ethanol.</p>
<p>Cellulosic ethanol’s path to <a href="http://www.bnet.com/blog/electric-cars/cellulosic-ethanol-8217s-time-may-finally-have-come/1475">commercialization</a>.</p>
<p>Could <a href="http://www.physorg.com/news201796104.html">termite spit</a> help?</p>
<p>Cellodextrin Transport in Yeast for Improved Biofuel Production, J.M. Galazka et al, Science, 10 Sept. 2010.</p>
</div>
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		<title>Pollinator crisis ahead</title>
		<link>http://whyfiles.org/2010/pollinator-crisis-ahead/</link>
		<comments>http://whyfiles.org/2010/pollinator-crisis-ahead/#comments</comments>
		<pubDate>Thu, 05 Aug 2010 20:58:26 +0000</pubDate>
		<dc:creator>admin</dc:creator>
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		<guid isPermaLink="false">http://whyfiles.org/?p=8928</guid>
		<description><![CDATA[Many of the tastiest crops can't pollinate themselves: melons, cucumbers, strawberries, almonds, cacao. But pollinators -- both native and managed -- are under threat from diseases and pesticides. They aren't finding enough to eat. Their colonies are dying. What can we do?]]></description>
			<content:encoded><![CDATA[Many of the tastiest crops can't pollinate themselves: melons, cucumbers, strawberries, almonds, cacao. But pollinators -- both native and managed -- are under threat from diseases and pesticides. They aren't finding enough to eat. Their colonies are dying. What can we do?]]></content:encoded>
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		<title>Tales of the whales</title>
		<link>http://whyfiles.org/2010/tales-of-the-whales/</link>
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		<pubDate>Thu, 15 Jul 2010 20:28:43 +0000</pubDate>
		<dc:creator>admin</dc:creator>
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		<guid isPermaLink="false">http://whyfiles.org/?p=8705</guid>
		<description><![CDATA[Some people blame strandings on a noisy ocean.  A new study shows that the endangered North Atlantic right whale is shouting to be heard. Another whale tale: a giant killing whale was recently discovered in Peru, with about the biggest teeth in history...]]></description>
			<content:encoded><![CDATA[Some people blame strandings on a noisy ocean.  A new study shows that the endangered North Atlantic right whale is shouting to be heard. Another whale tale: a giant killing whale was recently discovered in Peru, with about the biggest teeth in history...]]></content:encoded>
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		<title>Fish phishing attack explained!</title>
		<link>http://whyfiles.org/2010/fish-phishing-attack-explained/</link>
		<comments>http://whyfiles.org/2010/fish-phishing-attack-explained/#comments</comments>
		<pubDate>Thu, 07 Jan 2010 21:24:26 +0000</pubDate>
		<dc:creator>svmedaristwf</dc:creator>
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		<guid isPermaLink="false">http://whyfiles.org/?p=3983</guid>
		<description><![CDATA[Cleaner fish remove parasites from other fish. Why do males punish females who eat the wrong food from their host? A clue to the evolution of cooperation?]]></description>
			<content:encoded><![CDATA[<h3>Fishy, fishy: Errant cleaning lady gets punished!</h3>
<p>Many individuals engage in what social psychologists call &#8220;third-party punishment.&#8221; We may enforce social codes, even laws, related to marriage, sex, sexuality, vice and property. A classic example is a good Samaritan who ignores personal risk to chase a purse-snatcher.</p>
<p>Third-party punishment is so common that evolutionary psychologists suspect that it has genetic roots. Because punishment takes effort and can spark retaliation, it can only have evolved if it benefits the punisher: it can help the punisher reproduce (a direct benefit), or help the community survive (an indirect benefit).</p>
<p>Although the roots of human third-party punishment may have nothing to do with evolution, evolutionary psychologists often assume that its major benefit is indirect: I promote social stability by chasing a purse-snatcher. In stable society, I can have more children. Hence in evolutionary terms, chasing a purse-snatcher has indirect benefits.</p>
<div class="imgBigBlack"><a href="http://whyfiles.org/wp-content/uploads/2010/01/raihani2.jpg"><img class="aligncenter size-full wp-image-4032" title="Light blue fish with bright orange and yellow markings swimming with smaller fish nearby" src="http://whyfiles.org/wp-content/uploads/2010/01/raihani2.jpg" alt="Light blue fish with bright orange and yellow markings swimming with smaller fish nearby" width="620" height="432" /></a></p>
<div class="attrib">Courtesy Gerry Allen</div>
<div class="caption">Colorful cleaners: A pair of blue-streaked wrasses (<em> Labroides dimidiatus </em>) clean <em> Achanthurus mata</em>.</div>
</div>
<p>But in a study published this week, researchers found that third-party punishment directly benefits the punisher, at least when said punisher is  a &#8220;cleaner&#8221; fish. Cleaner fish eat parasites housed on larger fish, called &#8220;clients.&#8221; The relationship is classic symbiosis: the cleaner gets food, while the client stays healthy.</p>
<p>In the blue-streaked wrasse <em>Labroides dimidiatus</em> under study, males and females clean in pairs. Occasionally, a female cleaner switches from eating parasites to the more delectable mucus, a sticky goo that protects the client from infection.</p>
<p>(We sure swear to skirt slimy, sophomoric silliness and subsequently stick to the science.)</p>
<h3>Your cheatin&#8217; heart</h3>
<p>Behavioral ecologists call this &#8220;cheating&#8221; because it breaks the symbiosis and harms the client.</p>
<p>Redouan Bshary of the University of Neuchatel in Switzerland studies the wrasse in the Red Sea. He says a client typically swims into a &#8220;cleaning station&#8221; for about 20 seconds, where a male and female wrasse eat parasites from its exterior. When the female cheats, the client tends to get annoyed and swim to another cleaning station &#8211; unless the male wrasse darts at the female to keep her in line. That&#8217;s third-party punishment.</p>
<div class="box300black"><a href="http://whyfiles.org/wp-content/uploads/2010/01/raihani1.jpg"><img class="size-full wp-image-4031" title=" Grey fish with bright yellow fins swimming with a brown background" src="http://whyfiles.org/wp-content/uploads/2010/01/raihani1.jpg" alt=" Grey fish with bright yellow fins swimming with a brown background" width="300" height="450" /></a></p>
<div class="attrib">Courtesy Richard Smith</div>
<div class="caption">A blue-streaked wrasse cleans a member of the genus <em> Amblyglyphidodon</em></div>
</div>
<p>To test the situation in the lab, first author Nichola Raihani, a post-doctoral fellow at the London Zoological Society, smeared a Plexiglas plate with prawn meal or the less palatable fish flakes. When the females ate the prawn goop, the lab-keepers removed the plate and both fish confronted the sad sight of an empty menu.</p>
<p>When males responded aggressively to female cheating, the females were less likely to cheat again, reinforcing the notion that punishment would sustain the symbiosis and get him more food.</p>
<h3>Is punishment beautiful?</h3>
<p>Even though males were not directly harmed by the cheating, they directly benefited from the punishment, the authors wrote. &#8220;The establishment of self-serving third-party punishment in response to personal losses may be a key step toward third-party punishment without current involvement, as in humans.&#8221;</p>
<p>Scientists have observed punishment among other animals, says Katherine Cronin, a post-doctoral psychology research fellow who studies cooperation among monkeys at the University of Wisconsin-Madison. &#8220;Dominant rhesus monkeys might lash out at subordinates who didn&#8217;t properly alert them to food,&#8221; Cronin wrote us, &#8220;and female cowbirds (a species that lays eggs in other birds&#8217; nests to be reared by hosts) may seek out and destroy the eggs of hosts who have previously destroyed cowbird eggs in a surprisingly mafia-like fashion.&#8221;</p>
<p>Nonetheless, Cronin says, &#8220;careful, experimental demonstration of punishment in animals has been rare and requires creative experimental designs like the one employed by Raihani and colleagues.&#8221; Cronin notes that cleaner fish are cooperative. &#8220;The strongest examples of punishment might not come from the most cognitively complex animals, but rather from the ones that rely most heavily on cooperation to survive.&#8221;</p>
<div class="box300"><a href="http://whyfiles.org/wp-content/uploads/2010/01/good_behaviour_zone1.jpg"><img class="alignnone size-full wp-image-4030" title="Three street signs posted on brick fence in residential area, lowest one reading good behaviour zone" src="http://whyfiles.org/wp-content/uploads/2010/01/good_behaviour_zone1.jpg" alt="Three street signs posted on brick fence in residential area, lowest one reading good behaviour zone" width="300" height="430" /></a></p>
<div class="attrib">Photo: <a href="http://www.flickr.com/photos/futureshape/2614476028/">futureshape</a></div>
<div class="caption">The &#8220;good behavior&#8221; encouraged by this sign from the London (UK) police department may help the group and produce indirect benefits to the good-behaver. But in some cases, watching the behavior of others may also benefit the individual&#8230;</div>
</div>
<h3>Sexual politics, fish-style</h3>
<p>Exactly how does the male cleaner benefit from chasing misbehaving females? In most cases, we&#8217;d assume that keeping the food source (the client) around would constitute an evolutionary advantage because better-fed males can have more baby fishies, but we must remember that blue streaked wrasses are hermaphrodites. They begin reproducing as females, but females that grow large enough can turn into males.</p>
<p>Males can control this conversion, and avoid having another competitor for food, females and territory, by acting aggressively toward females, Bshary says. &#8220;If you remove the male, within two days, the female will show male behavior, and within a month, can release sperm that can fertilize eggs.&#8221;</p>
<p>And thus a male has an incentive to control the largest female in his harem, Bshary adds. &#8220;Typically the male tries to control her through aggression so she will not change sex. This is likely to be the main reason why the male responds aggressively to the female.&#8221;</p>
<h3>What&#8217;s the human impact?</h3>
<p>Whether the benefit is retaining food, a mate, or both, the study could shed light on puzzling human behaviors, says Raihani.  &#8220;Until now, most studies on third party punishment have tended to assume it stems from a group-level benefit.&#8221;</p>
<p>A group-level evolutionary explanation for a crime-fighting good Samaritan  would say that living in a crime-free society enables all people, including the Samaritan, to have more children. An individual-level explanation might suggest that the crime-fighting hero could gain social status, and therefore have a better choice of mates.</p>
<p>In the fish study, Raihani says, &#8220;We are trying to emphasize that you can get what looks like group-level behavior that evolves by individual selection.&#8221;</p>
<p>One final note, in case you thought the study is &#8220;just about fish.&#8221; The females are not the only fish who cheat, Raihani says. &#8220;Males cheat slightly more than females in this pair cleaning interaction, but females never  punish males, because they are so much smaller.</p>
<p>So the males can have their cake and eat it too.&#8221;</p>
<p>Sound familiar?</p>
<p>David J. Tenenbaum</p>
<div id="relateds">
<h3>Bibliography</h3>
<p>Punishers Benefit from Third-Party Punishment in Fish, Nichola J. Raihani, Alexandra S. Grutter and  Redouan Bshary, Science, 8 Jan. 2010.</p>
<h3>Related Why Files</h3>
<p>How many <a href="http://whyfiles.org/304ocean_b4fishing/">fish in the sea</a>?</p>
<p>Mammoth <a href="http://whyfiles.org/295marine_reserve/">marine</a> reserves: How useful?</p>
<p>Evolution: A <a href="http://whyfiles.org/shorties/269cichlid_evo/">fish story</a></p>
<p><a href="http://whyfiles.org/shorties/248fish_conserv/">Fishing</a>: the power of profit</p>
</div>
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		<title>Thanksgiving: What’s what with wild turkeys?</title>
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		<pubDate>Thu, 26 Nov 2009 17:39:49 +0000</pubDate>
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		<description><![CDATA[Turkeys got help for 75 years from conservation agencies. Coyotes spread across half the country all on their own.  Why have these animals succeeded? How have they changed the environment?]]></description>
			<content:encoded><![CDATA[Turkeys got help for 75 years from conservation agencies. Coyotes spread across half the country all on their own.  Why have these animals succeeded? How have they changed the environment?]]></content:encoded>
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		<pubDate>Thu, 15 Oct 2009 19:46:42 +0000</pubDate>
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		<description><![CDATA[Refuge is site of effort to use ultralight aircraft to guide crane chicks toward Florida wintering grounds. Dangers remain, but it's a step ahead for Americas' largest flying bird, once reduced to 21 animals.]]></description>
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		<title>At last: Parasites get some respect!</title>
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		<pubDate>Thu, 24 Jul 2008 20:44:19 +0000</pubDate>
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		<description><![CDATA[Along the coast of Baja, California, a new study finds that parasites outweigh top predators. What does this mean for ecology, and what is the story with "castrating parasites"?]]></description>
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