synthetic biology https://scienceblogs.com/ en Day 2 -- engineering life https://scienceblogs.com/esof2014/2014/06/23/day-2-engineering-life <span>Day 2 -- engineering life</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Today we get to the science and the issues surrounding it. Karl Deisseroth gave the first keynote lecture. For anyone who's been asleep the past few years, Deisseroth's lab at Stanford is at the cutting edge of a new kind of brain research. They invented optogenetics -- turning brain circuits on and off (in mice, at present) with fiberoptic lasers. Their lab is putting out new methodology at an astounding rate. Their latest is Clarity: a way of making the brain tissue clear, so you can see all the neurons at once. In other words, you can get an image of the whole brain. I know I am not the first person to see that image of the whole brain and feel somehow inspired in the same way that those people in the 1960s who saw the picture of the "whole earth" began to understand the planet differently.</p> <div style="width: 210px;"><a href="/files/esof2014/files/2014/06/image3.jpg"><img class="size-medium wp-image-62" src="http://scienceblogs.com/esof2014/files/2014/06/image3-200x300.jpg" alt="Karl Deisseroth" width="200" height="300" /></a> Karl Deisseroth </div> <p>And Karl is sort of your ideal scientist in an almost incredible way: He is also a psychiatrist who treats patients. So his research is ultimately about curing diseases like depression and autism. And he is as modest as a only scientist in his position can be; he emphasizes how much we still have to learn.</p> <p>But  he is unabashedly engineering not just the little optical fibers, but the mice, themselves. He has collaborations with engineers. And the technology they invent is open source -- they want labs around the world to adopt it, and they do. (disclaimer: one of his former postdocs, Ofer Yizhar, now has an optogenetics lab at the Weizmann Institute.) And he does think that some form of this technology could one day be used on humans.</p> <p>The second session I went to was on synthetic biology and society. I have to say that it looked more interesting in the abstract, in part because Drew Endy did not make it. The participants were the head of a plant biology lab, a head scientist in a biotech company, a British coordinator for synthetic biology research and a biohacker from Sunnyvale. I think that Karl Deisseroth might have had something to teach all of them about discovery and sharing.</p> <p>In part, I'm not sure that everyone was talking about the same biology. Getting yeast to produce vanilla is not quite the cutting edge of synthetic biology -- it probably verges on plain old genetic engineering, which is a less PC word. The cool factor of the biohacker was lessened a bit by a protestor who came to make a point about sexual harassment in the biohacker community, as well as his continued references to the Universe.  What I did find interesting and wanted to hear more about was the professor's involvement in the biohacker scene. He was the one who mentioned that biohackers have designed their own,  cheaper machinery, which they have then sold to others.  Also, I agree with them that some sort of synthetic biology is in our future, but I do have a problem with scientists who say:  "We are ethical, but what those Chinese do  with our findings, who who knows?" That discussion on whether the stakeholders ((ie you and me) have a say did not really happen.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> </div> <span><a title="View user profile." href="/author/judyhalper" lang="" about="/author/judyhalper" typeof="schema:Person" property="schema:name" datatype="">judyhalper</a></span> <span>Mon, 06/23/2014 - 05:23</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/guest-post" hreflang="en">guest post</a></div> <div class="field--item"><a href="/tag/science-event" hreflang="en">Science event</a></div> <div class="field--item"><a href="/tag/uncategorized" hreflang="en">Uncategorized</a></div> <div class="field--item"><a href="/tag/biohackers" hreflang="en">Biohackers</a></div> <div class="field--item"><a href="/tag/karl-desseiroth" hreflang="en">Karl Desseiroth</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <div class="field field--name-field-blog-categories field--type-entity-reference field--label-inline"> <div class="field--label">Categories</div> <div class="field--items"> <div class="field--item"><a href="/channel/social-sciences" hreflang="en">Social Sciences</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/esof2014/2014/06/23/day-2-engineering-life%23comment-form">Log in</a> to post comments</li></ul> Mon, 23 Jun 2014 09:23:11 +0000 judyhalper 143765 at https://scienceblogs.com Two New Directions in Synthetic Biology https://scienceblogs.com/weizmann/2012/05/23/two-new-directions-in-synthetic-biology <span>Two New Directions in Synthetic Biology</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>New online articles this week highlight two forays into the world of synthetic biology. Each, in its own way, gives a different perspective on how sophisticated the field has become in the past few years, since smiley-face DNA was first introduced.</p> <p>Prof. Benjamin Geiger of the Weizmann Institute and Prof. Joachim Spatz of the Max Planck Institute for Intelligent Systems, Germany are leading <a href="http://wis-wander.weizmann.ac.il/synthetic-cells-stand-in-for-the-real-thing" target="_blank">an unusual collaboration</a>. One is a biologist, the other a materials scientist. Together, they are working on models that incorporate the whole gamut from completely man-made materials to 100% biological cells. In between, they are creating synthetic cells – artificial lipid membranes with a handful of proteins added in.</p> <div class="mceTemp mceIEcenter" style="text-align: left;">The idea is to create a basic research model to study cell adhesion on various substrates. Cells are constantly checking their environment – continually assessing the surfaces they touch and deciding whether to adhere to those surfaces or pull up their adhesion complexes and move on. According to Geiger, scientists pretty much have the “grocery list” of which proteins are involved. But it is hundreds of proteins long – an extensive inventory of ingredients with no recipe attached. So Geiger and Spatz are looking for a way to recreate the recipe from the mixing bowl up: Adding a few proteins at time into their synthetic cells, they hope to understand which must come together for the basic process to occur, and which are enhancements and adjustments to the original formula.</div> <p>Of course much of human biology – growth and development, and cancer metastasis are the big ones – rely on these sensing and adhesion mechanisms, but Geiger and Spatz bring up some others: How certain cells sense blood flow, for instance, might affect the sticky buildup of plaques on artery walls. And they suggest that even before primitive cells began sticking together to form multicellular organisms, they probably formed some version of these complexes to adhere to other things – food sources, for instance.</p> <p><a href="http://wis-wander.weizmann.ac.il/matchmaker" target="_blank">The second article </a>describes the postdoctoral research and future plans of Dr. Sarel Fleishman, who recently joined the Institute. Fleishman was in the protein design lab of Prof. David Baker at the University of Washington, Seattle, where he designed a protein that is able to block a wide range of flu viruses.</p> <p>“Designed” is the operative word here: Fleishman and his lab mates showed that one can predict what is needed to selectively bind to a virus protein’s active site, create a detailed plan for a new protein structure to carry this out, and then actually shape that new protein according to plan on an existing protein base and even test it to see if it works. (Clearly, this one-sentence description makes it sound a lot simpler than it is.)</p> <p>Geiger and Spatz have been moving toward synthetic cell adhesion models for several years – beginning with putting live cells on precisely designed synthetic substrates to see how they react. So the synthetic cells, in one sense, are the next logical step in their investigations. They are betting that this step will be a significant one, however, and the European Research Council is laying down bets too, in the form of a hefty grant.</p> <p>Fleishman is now putting together his lab at the Institute. The protein he designed in his postdoctoral research is already on its way from the basic research bench to pharmaceutical R&amp;D. We can’t tell you what the next protein to come out of his new lab will be, or even whether the designer anti-flu protein will eventually end up on pharmacy shelves. But we can tell you that this is just the beginning.</p> <p dir="RTL" align="right"></p> </div> <span><a title="View user profile." href="/author/jhalper" lang="" about="/author/jhalper" typeof="schema:Person" property="schema:name" datatype="">jhalper</a></span> <span>Wed, 05/23/2012 - 06:11</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/research-model" hreflang="en">Research model</a></div> <div class="field--item"><a href="/tag/benjamin-geiger" hreflang="en">Benjamin Geiger</a></div> <div class="field--item"><a href="/tag/cell-adhesion" hreflang="en">cell adhesion</a></div> <div class="field--item"><a href="/tag/protein-design" hreflang="en">Protein design</a></div> <div class="field--item"><a href="/tag/sarel-fleishman" hreflang="en">Sarel Fleishman</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/weizmann/2012/05/23/two-new-directions-in-synthetic-biology%23comment-form">Log in</a> to post comments</li></ul> Wed, 23 May 2012 10:11:26 +0000 jhalper 71211 at https://scienceblogs.com SB 5.0 https://scienceblogs.com/oscillator/2011/06/14/sb-50 <span>SB 5.0</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-26e7974b09b3ed826e7ace7eb794923d-cheesecloth.jpg" alt="i-26e7974b09b3ed826e7ace7eb794923d-cheesecloth.jpg" /></p> <p>I'm making my way up to <a href="http://sb5.biobricks.org/">SB 5.0</a> for what promises to be a great conference. If you're going too, come say hi and smell some cheeses during the poster session!</p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Tue, 06/14/2011 - 04:20</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/synthetic-aesthetics" hreflang="en">synthetic aesthetics</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/06/14/sb-50%23comment-form">Log in</a> to post comments</li></ul> Tue, 14 Jun 2011 08:20:36 +0000 cagapakis 146972 at https://scienceblogs.com Re: Making Cellular Memories, a Guest Post https://scienceblogs.com/oscillator/2011/05/09/re-making-cellular-memories-a <span>Re: Making Cellular Memories, a Guest Post</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><em>Last month I <a href="http://scienceblogs.com/oscillator/2011/03/making_cellular_memories.php">wrote</a> about my friend Devin Burrill's <a href="http://genesdev.cshlp.org/content/25/5/434.abstract">paper</a> about synthetic memory in yeast cells. There were a lot of really interesting questions left in the comments, and I asked Devin if she would write a guest post to answer them. She agreed and here it is, answers to your questions straight from the author!</em></p> <p>Hello Readers!</p> <p>My name is Devin, and I am so incredibly grateful to Christina for allowing me to write an entry on her awesome blog. Christina and I are friends and work together in the lab of Pamela Silver at Harvard Medical School. I am writing in response to a number of excellent questions posted about Christina's entry on my recent paper, <a href="http://genesdev.cshlp.org/content/25/5/434.abstract">"Synthetic circuit identifies subpopulations with sustained memory of DNA damage"</a> (Burrill, et al. Genes &amp; Development, 2011).</p> <p><a href="http://scienceblogs.com/oscillator/2011/03/making_cellular_memories.php#comment-3504883">One reader asked</a> about the initiation of heritable damage responses: "Is damage restricted to random acts of nature, or can there be such a thing as self-damage....that will nevertheless be heritable?" </p> <p>DNA damage can come from within an organism, as well as from external sources. External sources tend to be obvious and well-known by the informed public (e.g. UV or IR radiation, drugs, smoking). Less obvious is the fact that pools of a DNA damaging reagent known as <a href="http://en.wikipedia.org/wiki/Reactive_oxygen_species">reactive oxidative species</a> (ROS for short) are created all the time by our own cells via mitochondrial respiration. </p> <p>Mitochondria are organelles that likely evolved from bacteria billions of years ago. They function as the "powerhouse" of the cell, generating cellular energy in the form of adenosine triphosphate (ATP) via the respiratory chain (RC) located at the inner mitochondrial membrane. Electrons move along the RC, reducing molecular oxygen at the end. If single electrons leave the RC earlier, ROS are generated. Incompletely reduced oxygen (superoxide radicals: O2-) can be transformed to H2O2, then leading to free hydroxyl radicals. Hydroxyl radicals are one of the most damaging forms of ROS, mutating the DNA backbone and even the DNA bases themselves. This source of internal DNA damage is simply part of a cell's natural biochemistry. As people age, however, ROS production tends to worsen because the mitochondria also age and become less efficient at tracking electrons all the way along the RC. This source of internal damage is actually hypothesized to be a main contributor toward the human aging process --- as promiscuous ROS production increases, so to does DNA damage caused by ROS, resulting in dysfunctional biological processes. Thus, damaged mitochondria are inherited over time as people age, though the exact mechanisms are how this happens are not completely understood. </p> <p><a href="http://scienceblogs.com/oscillator/2011/03/making_cellular_memories.php#comment-3755762">Another reader asked</a> about the nature of the observed cellular memory: "Do the cells that retain this memory of an experience then pass on that memory to those they have been divided into?...And how many generations does this affect?" Yes, the idea is that a single cell experiences the damage and responds in a specific way which is somehow recorded, thus changing the cell's biological makeup. We were interested in changes that were subsequently passed on to daughter cells when the original cell divided. The fluorescent memory loop allowed us to track the damage response from the original cell that experienced it to the daughter cells. We tracked the response for 48 hours after DNA damage, which means that the original cell divided approximately 20 times, resulting in lots of fluorescent daughter cells. A sustained response that lasts 20 cell generations is remarkable, given the propensity of the yeast <em>S. cerevisiae</em> to re-set its biological clock when its divides. However, one could imagine studying the response for even longer periods of time. There's really no limit!</p> <p>The same reader then went on to ask a very important question, which really gets at the meat of the project: "Can the effects of this experience ever be completely erased from the genome if the experience itself is replicated or repeated in a particular environment? And is this perhaps one of the ways that cells evolve to anticipate and deal strategically with a multitude of problems?" I believe the reader is asking whether experiencing and responding to the damage once can impact how the cell responds to the same experience if it happens again. This question brings forward the idea of biological <a href="http://en.wikipedia.org/wiki/Hysteresis">hysteresis</a> --- does a past event allow a cell or system to respond differently to future events because memory of the past event persists? It's possible that initial exposure could result in heritable epigenetic marks or stable cytoplasmic factors, for example, that will permit a "better" response to a second exposure of the same damaging agent. While some previous work has looked at cellular responses to multiple doses of damaging agents, these studies are flawed by the fact that they take place at the whole population level, thereby diluting out any long-term effects that occur within distinct subpopulations. Now that we have engineered a device that allows for the isolation of two distinctly-responsive subpopulations, we can more properly examine the role of hysteresis in DNA damage response. Will one subpopulation respond better to a second dose of damage? If the system were moved to mammalian cells, would one subpopulation be more resistant or susceptible to multiple rounds of chemotherapy? In our paper, we laid the groundwork for exploring these questions and are now pursuing these very lines of research.</p> <p>I cannot say how exciting it is to get questions like the ones proposed by Christina's readers. They are very thoughtful and insightful. Thank you so very much for asking them, and thank you for letting me answer them! </p> <p>Take care!</p> <p>---- Devin</p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Mon, 05/09/2011 - 09:06</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/dna" hreflang="en">DNA</a></div> <div class="field--item"><a href="/tag/friends" hreflang="en">friends</a></div> <div class="field--item"><a href="/tag/memory" hreflang="en">memory</a></div> <div class="field--item"><a href="/tag/research" hreflang="en">Research</a></div> <div class="field--item"><a href="/tag/scientists" hreflang="en">Scientists</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2494154" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1305050175"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I'm the guy that asked the questions about cell memory and it's apparent evolutionary role in what seems to me to be the development of instinctive and anticipatory adaptive strategies.<br /> Your answers have been very helpful, especially as this is close to the verboten subject of Lamarckian mechanisms, which it seems most researchers would rather investigate anew than talk about. Especially here on ScienceBlogs.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494154&amp;1=default&amp;2=en&amp;3=" token="1AkzkRla49KPAFXKSazfm215Iwan5nSsCKxt_Rr2zHQ"></drupal-render-placeholder> </div> <footer> <em>By <a rel="nofollow" href="http://realfiction.blogspot.com/" lang="" typeof="schema:Person" property="schema:name" datatype="">Roy Niles (not verified)</a> on 10 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494154">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494155" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1305132030"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>In regards to cell memory and heritable traits, would organisms which more readily demonstrate an ability to produce a trait become more prevalent given a particular set of environmental stimuli. In short a set of characteristics within a population may repeat, but only be of concern if presented with specific environmental stimuli, at which point the entire population would not be at risk but rather different parts of the population would survive or die depending on the stimulus. "We Beasties," has a recent blog discussing how ROS can add to the aging process, but can also be used to fight certain bacterial infections: Given that info, without a bacterial stimulus ROS is a maladaptation and leads to a shorter life...with a bacterial infection ROS leads to a better resistence and an ability to survive that would otherwise not be present. Just trying to wrap my mind around it....feel free to correct comment or laugh hysterically at my lack of understanding. In the event of laughter, however, please explain my idiocy in monosyllables so I'll understand...if possible.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494155&amp;1=default&amp;2=en&amp;3=" token="S5RKvArTenjM7WMMUsxX63h4U2rCtDyttnaiaFG8wHQ"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Mike Olson (not verified)</span> on 11 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494155">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/05/09/re-making-cellular-memories-a%23comment-form">Log in</a> to post comments</li></ul> Mon, 09 May 2011 13:06:26 +0000 cagapakis 146969 at https://scienceblogs.com Bio:Fiction https://scienceblogs.com/oscillator/2011/04/25/biofiction <span>Bio:Fiction</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Two videos that <a href="http://twitter.com/#!/p_maverick_b">Patrick Boyle</a> and I made were selected for the <a href="http://bio-fiction.com/en/">Bio:Fiction</a> Film Festival! One of the prizes is an <a href="http://bio-fiction.com/videos/">online audience award</a>, and you can watch and rate all of the films! It's such an honor to be part of this festival and to be showing our work next to that of so many amazing artists, scientists, and filmmakers, and we would be super thrilled if you <a href="http://bio-fiction.com/videos/">voted for us</a>!</p> <p>Here are our videos! First, the world premiere of <em>Compound 74</em>, a fictional documentary about a possible future of synthetic drug design through synthetic biology:</p> <iframe title="YouTube video player" width="510" height="300" src="http://www.youtube.com/embed/lQjF8ir4SKs" frameborder="0" allowfullscreen=""></iframe><p> And second, the <a href="http://scienceblogs.com/oscillator/2010/09/meet_ginkgo_bioworks.php">commercial we made</a> for <a href="http://ginkgobioworks.com/">Ginkgo BioWorks</a>--<em>Who is the Engineer of the Future?</em></p> <iframe title="YouTube video player" width="510" height="300" src="http://www.youtube.com/embed/q7fpwmQWCkA" frameborder="0" allowfullscreen=""></iframe><p> <a href="http://bio-fiction.com/videos/">Please vote!</a></p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Mon, 04/25/2011 - 11:56</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/announcement" hreflang="en">Announcement</a></div> <div class="field--item"><a href="/tag/art" hreflang="en">Art</a></div> <div class="field--item"><a href="/tag/culture" hreflang="en">Culture</a></div> <div class="field--item"><a href="/tag/drugs" hreflang="en">Drugs</a></div> <div class="field--item"><a href="/tag/fun" hreflang="en">fun</a></div> <div class="field--item"><a href="/tag/plug" hreflang="en">plug</a></div> <div class="field--item"><a href="/tag/systems-biology" hreflang="en">systems biology</a></div> <div class="field--item"><a href="/tag/video" hreflang="en">Video</a></div> <div class="field--item"><a href="/tag/film-festival" hreflang="en">film festival</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> <div class="field--item"><a href="/tag/technology" hreflang="en">Technology</a></div> <div class="field--item"><a href="/tag/voting" hreflang="en">voting</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2494141" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303891360"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Love it, Christina! Very cool - congratulations. Hope all is well.<br /> -AB</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494141&amp;1=default&amp;2=en&amp;3=" token="jpA01KjhNmjKF9C0w6fTB5QgaQflAFWotxozSvDtXbI"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Adam B. (not verified)</span> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494141">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494142" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303897732"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I voted! My designer friends Daisy and James have video's up too, so I'll probably be blogging about it tomorrow :D</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494142&amp;1=default&amp;2=en&amp;3=" token="PQsQ05oWVof9VQQpZWmkUxcsXa1CjhH7JFxfiixhqpQ"></drupal-render-placeholder> </div> <footer> <em>By <a rel="nofollow" href="http://labrat.fieldofscience.com/" lang="" typeof="schema:Person" property="schema:name" datatype="">Lab Rat (not verified)</a> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494142">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494143" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303910060"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>After watching most of the other submissions I found there were only one or two that could compare to 'compound 74'; definitely 5 stars for it. Excellent, entertaining work. Thanks!</p> <p>'Ginkgo BioWorks' was also good, but a bit corny though. 4, because it was a funny corny.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494143&amp;1=default&amp;2=en&amp;3=" token="Z-_jEtN4R1fmcseYWrbURc5HSp89crZa9PWkKkphwIc"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">superkuh (not verified)</span> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494143">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494144" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303922622"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Trouble is, the videos are presented in Flash which is a dead technology. Many hundreds of thousands of people cannot see any Flash content because they've wisely chosen to turn it off in their web browser or because they use Apple produts, and Apple has turned it off for them. Get with the program and move to HTML-5</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494144&amp;1=default&amp;2=en&amp;3=" token="31jViLvZnqG_yFWKAxg0Z1NGStiuV-nC4bHVWjzDnqM"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Don Markovski (not verified)</span> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494144">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="307" id="comment-2494145" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303923027"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>The videos are embedded from Vimeo, which I think is changing over a lot of their videos to be HTML5 eventually. For now, I have flash disabled on my mac and I use this plugin to load youtube and vimeo videos in HTML5 instead of flash and it works great!<br /><a href="http://www.verticalforest.com/2010/10/27/youtube5-version-2/">http://www.verticalforest.com/2010/10/27/youtube5-version-2/</a></p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494145&amp;1=default&amp;2=en&amp;3=" token="rX5kE8FRsTz0-lPjAGoqSG_2Pk6fW4tof3YpEcZwmRs"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494145">#permalink</a></em> <article typeof="schema:Person" about="/author/cagapakis"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/cagapakis" hreflang="en"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494146" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304543700"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Why "compound 74"?<br /> This has been suggested as a very serious answer to the war on drugs via modifying ephedra derived biology in order to produce methamphetamine "yoghurt":<br /><a href="http://www.science20.com/alpha_meme/adhd_yoghurt_winning_drug_war">http://www.science20.com/alpha_meme/adhd_yoghurt_winning_drug_war</a></p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494146&amp;1=default&amp;2=en&amp;3=" token="s1Kq204OitlNdmVIh01PNoNd6SqhdP2_dUnWaAk3n48"></drupal-render-placeholder> </div> <footer> <em>By <a rel="nofollow" href="http://www.science20.com/alpha_meme" lang="" typeof="schema:Person" property="schema:name" datatype="">Sascha Vongehr (not verified)</a> on 04 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494146">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/04/25/biofiction%23comment-form">Log in</a> to post comments</li></ul> Mon, 25 Apr 2011 15:56:23 +0000 cagapakis 146967 at https://scienceblogs.com (Photo)Synthetic Endosymbiosis https://scienceblogs.com/oscillator/2011/04/20/synthetic-endosybiosis <span>(Photo)Synthetic Endosymbiosis</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><a href="http://en.wikipedia.org/wiki/Lichen"><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-2cdd23c75a377b0e355660cf7f7f8f12-Haeckel_Lichenes-thumb-250x348-63896.jpg" alt="i-2cdd23c75a377b0e355660cf7f7f8f12-Haeckel_Lichenes-thumb-250x348-63896.jpg" /></a><a href="http://en.wikipedia.org/wiki/Symbiosis">Symbiosis</a> is everywhere. From the Greek for "living with," symbiosis is simply a close association between two different species in nature. These relationships can be mutualistic, parasitic, or somewhere in between. Bacterial symbionts live inside bodies, like the bacteria that help us and <a href="http://en.wikipedia.org/wiki/Rumen#Microbes_in_the_reticulorumen">other animals digest our food</a>, and they live inside cells, like the bacteria that <a href="http://en.wikipedia.org/wiki/Rhizobia">live in plant roots and provide their hosts with nitrogen</a>. They can be metabolic, <a href="http://en.wikipedia.org/wiki/Cleaner_fish">hygienic</a>, or photosynthetic; ectosymbiotic, on the host surface, or endosymbiotic, inside the host's cells. Back in the 1860's biologists considered each organism to be an individual, autonomous whole, but the Swiss botanist Simon Schwendener observed that lichen is actually an association between two different types of cells, a fungus and a photosynthetic algae. Shortly after that, other botanists began to notice that the chloroplasts, the organelles that provide photosynthetic power to plant cells, resembled free-living photosynthetic bacteria. It took several decades and the rise of molecular biology to learn that these organelles had their own DNA, and to convince scientists that they had started out as bacteria.</p> <p>Photosynthetic endosymbiosis created plants and still exists in many other organisms and in many forms today. The sea slug <em><a href="http://en.wikipedia.org/wiki/Elysia_chlorotica">Elysia chlorotica</a></em> is one of the best known examples. It rips the chloroplast organelles out of the algae that it eats and incorporates them into its highly branched digestive system, able to live off of sunlight harvested by these symbionts for several months.<br /><a href="http://en.wikipedia.org/wiki/Elysia_chlorotica"><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-e9a5ec851a181dd4bfb8d7d7f831a5b4-Elysia_chlorotica-thumb-350x187-63898.jpg" alt="i-e9a5ec851a181dd4bfb8d7d7f831a5b4-Elysia_chlorotica-thumb-350x187-63898.jpg" /></a>Almost all of the photosynthetic endosymbiotic relationships known show up in invertebrates that don't move a lot and have a very high surface-to-volume ratio, resembling very slow-moving leaves. But all this changed a <a href="http://www.wired.com/wiredscience/2011/04/symbiotic-salamander/">couple weeks ago</a> with the publication of a really cool <a href="http://www.pnas.org/content/early/2011/03/29/1018259108">paper</a>. Ryan Kerney and his colleagues were studying a species of salamander that is known to be associated with algae during its embryonic stage. What they found was that contrary to what had been reported before, the algae were living <em>inside of the salamander cells</em>!</p> <p><a href="http://www.pnas.org/content/early/2011/03/29/1018259108"><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-35288e0b1039c8d14f0acbb49409ad90-salamander-thumb-400x386-63902.jpg" alt="i-35288e0b1039c8d14f0acbb49409ad90-salamander-thumb-400x386-63902.jpg" /></a></p> <p>The relationship between the salamander and the algae is especially interesting because it shows just how wide the range of situations where endosymbiosis can happen. In one extreme, the slug can't survive without the algae and actually becomes photosynthetic, while the salamander can develop just fine without any algae, does not harvest any energy from the algae, and lives most of its adult life underground, away from sunlight.</p> <p>In my lab, a lot of people study photosynthetic bacteria like the ones that eventually became the plant chloroplast through endosymbiosis. Projects range from basic cell biology and understanding the <a href="http://scienceblogs.com/oscillator/2010/03/carboxysome_in_a_row.php">internal organization of the bacteria</a> to trying to engineer them to produce useful chemicals. A couple years ago, a very awesome and very talented master's student, Henrike Niederholtmeyer (her awesomeness is directly proportional to the number of syllables in her name), was working on engineering these cyanobacteria to produce sugar. </p> <p>The bacteria typically grow in fresh water, and putting them in salt water can put a lot of pressure one their membranes. To protect themselves, the bacteria produce sucrose (table sugar), which helps to balance out the osmotic pressure. What Henrike did was engineer the bacteria with invertase, the gene that splits sucrose into glucose and fructose, and with a transporter gene that lets the sugar leave the inside of the cell. Now, when the bacteria are put in salt water, they secrete sugars out into environment. It isn't a ton of sugar, but it's enough to create a symbiotic relationship between <em>E. coli</em> (yellow cells, red line) and the cyanobacteria (red cells):</p> <p><a href="http://aem.asm.org/cgi/content/abstract/76/11/3462"><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-b2384bc9e9737e9c4594a5a771883cd5-crossfeeding-thumb-400x165-63892.png" alt="i-b2384bc9e9737e9c4594a5a771883cd5-crossfeeding-thumb-400x165-63892.png" /></a></p> <p>This got Henrike and my advisor, <a href="https://silver.med.harvard.edu/">Pam Silver</a>, thinking about how photosynthetic symbiosis is established and how we could re-create it in the lab. At this point, I was fascinated, and convinced Henrike to let me tag along on the experiment. How could we get the cyanobacteria inside of animal cells to establish a synthetic endosymbiosis?</p> <p>We were lucky to be in a very creative and supportive lab and department and to have one of the best zebrafish labs anywhere right down the hall. <a href="https://wiki.med.harvard.edu/SysBio/Megason/">Sean Megason's group</a> studies the development of zebrafish embryos and uses powerful microscopes to track every cell as the fish grows. Zebrafish are also relatively easy to microinject (if you are a professional) and clear, letting light into their cells that the cyanobacteria would need to grow. Henrike hooked Ramil Noche, a postdoc in the Megason lab, the same way she hooked me into the project, and his zebrafish skills are unmatched. He injected fresh zebrafish eggs with millions of wild-type cyanobacteria, put them in the incubator, and we waited.</p> <p>The biggest surprise was that <em>nothing happened</em>. The embryos developed normally into a happy, swimming fish when we injected them with cyanobacteria. Even after 1 hour we could see that something was up, since the cyanobacteria-injected embryo looked normal (panel A, a red dye is used during injections to keep track of which ones are done which is why the embryo looks red), while injecting <em>E. coli</em> had a quite drastic result (panel B).</p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-7d9ebfeb9a70be70ac61fa680a533bf2-zebrafisheggs.jpg" alt="i-7d9ebfeb9a70be70ac61fa680a533bf2-zebrafisheggs.jpg" /></p> <p>While the sugar secretors were the inspiration to try this experiment, they don't produce nearly enough sugar to actually support a living animal cell, and all of these pictures show normal, un-engineered cyanobacteria inside of the fish. These fish are not photosynthetic, they just live happily with photosynthetic bacteria inside of their own cells. The zebrafish cell membranes are engineered to be green fluorescent, and the green pigments in the cyanobacteria cells fluoresce red, so they look like little red dots in the images:</p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-b28da5f03ee8dd74009f62441a0337ee-embryo.jpg" alt="i-b28da5f03ee8dd74009f62441a0337ee-embryo.jpg" /></p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-606f6c362399599a8e2c3675979ed9a9-zebrafish.jpg" alt="i-606f6c362399599a8e2c3675979ed9a9-zebrafish.jpg" /></p> <p>Here's one of the amazing images that Ramil took with the confocal microscope, where you can look at just a single plane of the fish, looking into the cells themselves. This image is of the head of a live two-day old embryo, and you can see red dots of where the bacteria are inside its eye and brain:</p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-0357a8e90f94dfafd5fb627e4d5d0058-confocal.jpg" alt="i-0357a8e90f94dfafd5fb627e4d5d0058-confocal.jpg" /></p> <iframe title="YouTube video player" width="510" height="415" src="http://www.youtube.com/embed/IjDE9Ycz6y8" frameborder="0" allowfullscreen=""></iframe><p> This result inspired me and Henrike to try and get the cyanobacteria into other cells. Some synthetic biologists are trying to create <a href="http://www.technologyreview.com/biomedicine/16949/?mod=related&amp;a=f">tumor killing bacteria</a>, that can seek out cancer cells, <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-4HJRXGD-4&amp;_user=10&amp;_coverDate=01%2F27%2F2006&amp;_rdoc=1&amp;_fmt=high&amp;_orig=gateway&amp;_origin=gateway&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=04bed7b37092f4061bc9bd7c9fe7ade7&amp;searchtype=a">get inside of them</a> and specifically kill only those cells, leaving healthy cells intact. They engineer these bacteria with a gene called invasin that, as the name implies, allows them to invade mammalian cells. A second gene called listeriolysin is needed for the bacteria to escape the membrane-bound compartment that they get stuck inside, and to get into the cytoplasm. Engineering the cyanobacteria with these two genes allowed them to invade hamster cells in culture at a low but appreciable efficiency. </p> <p>Listeriolysin also lets the bacteria escape from the digestive forces of macrophages, a type of immune cell that can capture and eat up bacteria. When we had mouse macrophages swallow up the engineered cyanobacteria, we saw them escape digestion and slowly start dividing, a first step for establishing a symbiosis. In the video, taken by Tami Lieberman, you can see the macrophages with the engineered cyanobacteria in them. On the left is the dish in the dark, and the white dots are the bacteria, which slowly die overnight without any light to support them. On the right the light is on, and after a while, one of the red bacteria divides into two:</p> <iframe title="YouTube video player" width="510" height="300" src="http://www.youtube.com/embed/NFdkVmaDZtM" frameborder="0" allowfullscreen=""></iframe><p> Again, these mouse cells aren't photosynthetic, but these experiments show how photosynthetic bacteria can develop special relationships with animal cells. Because they aren't pathogens and don't need to steal nutrients from their host cell, these kinds of benign symbiotic associations are possible. The wide range of symbiotic possibilities found in nature can inspire synthetic biologists like us to explore and re-create these kinds of relationships as a way to study the evolution of symbiosis or as a way to design new multi-species biological behaviors greater than the sum of their parts. Endosymbiosis drove the evolution of the eukaryotic kingdom with the mitochondria and the chloroplast, perhaps endosymbiosis will play a role in the evolution of the <a href="http://www.daisyginsberg.com/projects/synthetickingdom.html">synthetic kingdom</a> as well.</p> <p>You can check out our paper in PLoS ONE, out today! <a href="http://dx.plos.org/10.1371/journal.pone.0018877">Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. "Towards a Synthetic Chloroplast." </a></p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Wed, 04/20/2011 - 11:00</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> <div class="field--item"><a href="/tag/experiment-0" hreflang="en">experiment</a></div> <div class="field--item"><a href="/tag/papers" hreflang="en">papers</a></div> <div class="field--item"><a href="/tag/research" hreflang="en">Research</a></div> <div class="field--item"><a href="/tag/symbiosis" hreflang="en">symbiosis</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> <div class="field--item"><a href="/tag/video" hreflang="en">Video</a></div> <div class="field--item"><a href="/tag/news" hreflang="en">News</a></div> <div class="field--item"><a href="/tag/photosynthesis" hreflang="en">photosynthesis</a></div> </div> </div> <div class="field field--name-field-blog-categories field--type-entity-reference field--label-inline"> <div class="field--label">Categories</div> <div class="field--items"> <div class="field--item"><a href="/channel/life-sciences" hreflang="en">Life Sciences</a></div> </div> </div> <section> <article data-comment-user-id="132" id="comment-2494135" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303386142"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>w00t! Congratulations! Great paper and great blog post!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494135&amp;1=default&amp;2=en&amp;3=" token="1pFZMqLk6suuJEv_f8Bk6fmDZCIBeXGB70wsX5cjOeE"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/Bora-Zivkovic" lang="" about="/author/Bora-Zivkovic" typeof="schema:Person" property="schema:name" datatype="">clock</a> on 21 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494135">#permalink</a></em> <article typeof="schema:Person" about="/author/Bora-Zivkovic"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/Bora-Zivkovic" hreflang="en"><img src="/files/styles/thumbnail/public/pictures/Bora%20Zivkovic.jpg?itok=QpyKnu_z" width="75" height="100" alt="Profile picture for user clock" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494136" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1303894217"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I absolutely love how you place your research into context here. It preemptively buffers the potential gee-whiz sensationalism and misinformed panic that is often sparked when out-of-the-box studies like this are published. Your blog is not only educational and enjoyable to read, it's very responsible. This is a very good model for researcher-public communication.</p> <p>This blog post would actually make an excellent addition to a thesis. :)</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494136&amp;1=default&amp;2=en&amp;3=" token="zLh4ZCTcqYbdYmHY9ceKt-t7eBZveYBrjsnP0ZDHi04"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Karmella (not verified)</span> on 27 Apr 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494136">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494137" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304897251"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I was reading "We Beasties," and a poster mentioned you...this is great stuff, thanks for posting it.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494137&amp;1=default&amp;2=en&amp;3=" token="leupvJenUCVZIdBkNAYSkpCy2cZZY4XhZXw0lGidETc"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Mike Olson (not verified)</span> on 08 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494137">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="281" id="comment-2494138" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304931201"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Oh great, another RSS feed to keep from from getting my PhD done. Thanks a lot :-P</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494138&amp;1=default&amp;2=en&amp;3=" token="QSnspjb9mn6V5FyDJia52lky4v3NrjrrQJpd-lZRodI"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/kbonham" lang="" about="/author/kbonham" typeof="schema:Person" property="schema:name" datatype="">kbonham</a> on 09 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494138">#permalink</a></em> <article typeof="schema:Person" about="/author/kbonham"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/kbonham" hreflang="en"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="105" id="comment-2494139" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1305147279"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>This is great! It reminds me of when I was a post-doc trying to electroporate Trypanosomes with Agrobacterium. It was one of those things that seemed like a good idea at the time but didn't have anywhere near the elegance of microinjecting DNA.</p> <p>Very nice!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494139&amp;1=default&amp;2=en&amp;3=" token="5ZZSN1eUXf8tDj4aoUVw7jIeMiQPAJtr1Co4ev32WIo"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/sporte" lang="" about="/author/sporte" typeof="schema:Person" property="schema:name" datatype="">sporte</a> on 11 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494139">#permalink</a></em> <article typeof="schema:Person" about="/author/sporte"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/sporte" hreflang="en"><img src="/files/styles/thumbnail/public/pictures/59121-arsenic_protein-150x150-120x120.png?itok=o0ajJdDI" width="100" height="100" alt="Profile picture for user sporte" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494140" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1337071437"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Perhaps this sort of experiment could be repeated with a strain of Chlorella or Chloroccous that has already endosymbiotized something else (paramecia bursaria for example). The cells could then be put into melanocytes which would inject them into the normal keratocytes thereby spreading the "infection" into other cells. I think though that part of the answer to getting the cells to be stable in-entero would be to leave them inside the vacoule membrane. Get the DV to differentiate into a Perialgal vacuole. This could potentially mask the LPS that is in their surface.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494140&amp;1=default&amp;2=en&amp;3=" token="UEMi5Z0BjJ2w6I54SkoksAjkFc82XP438yzS34I3tqo"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Neale Haugen (not verified)</span> on 15 May 2012 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494140">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/04/20/synthetic-endosybiosis%23comment-form">Log in</a> to post comments</li></ul> Wed, 20 Apr 2011 15:00:00 +0000 cagapakis 146965 at https://scienceblogs.com Synthetic Biology Slam https://scienceblogs.com/oscillator/2011/04/16/synthetic-biology-slam <span>Synthetic Biology Slam</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Before you get your tickets for <a href="http://sb5.biobricks.org/">SB 5.0</a> make sure that you'll be in town for the world's first Synthetic Biology Slam!</p> <p><a href="http://scienceblogs.com/oscillator/r6ded.jpg"><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-742e2d71a64187e591bab8147b583142-r6ded-thumb-510x660-63795.jpg" alt="i-742e2d71a64187e591bab8147b583142-r6ded-thumb-510x660-63795.jpg" /></a></p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Sat, 04/16/2011 - 12:29</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/announcement" hreflang="en">Announcement</a></div> <div class="field--item"><a href="/tag/fun" hreflang="en">fun</a></div> <div class="field--item"><a href="/tag/plug" hreflang="en">plug</a></div> <div class="field--item"><a href="/tag/poetry" hreflang="en">Poetry</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/04/16/synthetic-biology-slam%23comment-form">Log in</a> to post comments</li></ul> Sat, 16 Apr 2011 16:29:22 +0000 cagapakis 146964 at https://scienceblogs.com Making Cellular Memories https://scienceblogs.com/oscillator/2011/03/11/making-cellular-memories <span>Making Cellular Memories</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Cells permanently change their behavior in response to temporary changes to the environment, a kind of biological memory that controls processes as important and complex as how stem cells differentiate into specific tissues or how the immune system "remembers" dangerous pathogens. At its simplest, cellular memory is achieved with a positive feedback loop--once activated by some external signal, the feedback loop will continually activate itself, even as the cell divides and the signal is taken away. In synthetic biology we can recreate such simple feedback loops, genetic circuits built of parts that activate in response to signals and keep turning themselves on, remembering past chemical events. A few years ago in my lab, David Drubin and Caroline Ajo-Franklin made such a <a href="http://genesdev.cshlp.org/content/21/18/2271.full">synthetic genetic device in yeast that remembers</a> if the cells have been grown in media containing the sugar galactose. </p> <p>They connected genetic elements that turn on when the cells taste galactose to a protein that fluoresces red and to a protein that activates the synthetic positive feedback loop. The positive feedback loop in turn is made of a protein that fluoresces yellow and the protein that activates the loop, starting a permanent cycle of feedback. In the video below you can see the red protein turn on and then off again as the galactose is removed, but the yellow protein (which looks green in the video) stays on in the population, even as the cells divide and grow:</p> <iframe title="YouTube video player" width="480" height="390" src="http://www.youtube.com/embed/nlqltVI2jSc" frameborder="0" allowfullscreen=""></iframe><p> We don't usually need to know whether or not cells have tasted galactose, but the parts of the synthetic circuit are modular, they can be swapped out and activated with different triggers to create larger networks of interconnected feedback loops to create more complicated behaviors, or to ask questions about cell biology. </p> <p>In galactose almost all of the cells responded and turned on the feedback loop, but in more natural conditions, for example in tissues in the body or in mixed populations of microorganisms in the environment, cellular responses to signals are rarely uniform. When radiation or carcinogens damage cells' DNA in a tissue, some cells may have more mutations and more strongly activate the cellular stress response to fix their DNA. These different responses to DNA damage between different cells show up even in populations of single-celled organisms and can have implications for how we understand cancer progression, where a cell's response to DNA mutation can have an impact on whether or not that cell starts dividing out of control. </p> <p>My awesome labmate Devin wanted to use synthetic memory to be able to track yeast cells that "remembered" having experienced significant DNA damage, to study how they are different from their neighbors that escaped with minimal mutations. She swapped out the genetic part that tastes galactose in the old yeast memory circuit to one that turns on when the cell's DNA is mutated by radiation or chemical carcinogens, cutely and somewhat strangely named HUG1. When she poisoned the yeast cells that had the synthetic memory in place with EMS, a chemical that causes DNA mutations, she saw something very similar to the previous memory circuit. The red fluorescent protein (RFP) stayed on for a short time after the carcinogen was washed off of the cells, but the yellow protein (YFP) stayed on for several days after that, identifying cells that remembered the DNA damage and their offspring.</p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-10d8e2053c764713ec2aa01edeb1b30d-memorycells.png" alt="i-10d8e2053c764713ec2aa01edeb1b30d-memorycells.png" /></p> <p>This is already pretty cool, but the really interesting part of the story started when she started to study how the cells that remembered the damage were different from the ones that didn't. Because the memory cells were fluorescent, she could use <a href="http://en.wikipedia.org/wiki/Fluorescence-activated_cell_sorting#Fluorescence-activated_cell_sorting">fluorescent activated cell sorting</a> to sort the two populations, the dim cells that didn't experience as many mutations from the bright cells that were harder hit. </p> <p>While the dim cells were indistinguishable from yeast cells that had never been mutagenized, the fluorescent cells grew much slower and had a very different mutation rate. As cells divide and grow there is always a low percentage of mutations, even without carcinogens, errors that arise in the copying of the DNA. We can get an estimate of how many random mutations there are by seeing how many cells out of a billion will mutate to a different behavior, like being able to grow in conditions that are typically bad for the cell. Devin found that even many generations after the mutagen was removed, the fluorescent cells that remembered the chemical had a much lower rate of mutation. Remembering the past DNA damage left them hyper-vigilant against future mutations, keeping the stress response that can fix mutations active and the mutation rate low. </p> <p><img src="http://scienceblogs.com/oscillator/wp-content/blogs.dir/343/files/2012/04/i-28299e53000f1577c00777b3fec58f9c-memorymodel.png" alt="i-28299e53000f1577c00777b3fec58f9c-memorymodel.png" /></p> <p>This <a href="http://en.wikipedia.org/wiki/Hormesis">hormesis</a>--a beneficial response to a low dose of a toxin--would be impossible to detect without the synthetic memory, especially since the slower growth rate of the memory cells would dilute them out of the population as the cells grew. Synthetic biology often uses metaphors from computers to help understand and promote the field, including when it comes to memory. But biological memory can do a lot more than store bits, it can help us to understand something fundamental about how cells work.</p> <p>You can check out Devin's amazing paper here: "<a href="http://genesdev.cshlp.org/content/25/5/434.abstract">Synthetic circuit identifies subpopulations with sustained memory of DNA damage</a>," Genes and Development 25: 434-439, 2011.</p> </div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Fri, 03/11/2011 - 09:21</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/friends" hreflang="en">friends</a></div> <div class="field--item"><a href="/tag/memory" hreflang="en">memory</a></div> <div class="field--item"><a href="/tag/papers" hreflang="en">papers</a></div> <div class="field--item"><a href="/tag/research" hreflang="en">Research</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> <div class="field--item"><a href="/tag/research-blogging-0" hreflang="en">research blogging</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2494123" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1299874079"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Super interesting!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494123&amp;1=default&amp;2=en&amp;3=" token="PEVeDuWTsCTrFeDe2GM621JyerJ8rWIfvvzOa8ccUjg"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Cyan (not verified)</span> on 11 Mar 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494123">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494124" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1299895730"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I feel like there must be a way to build an organic computer out of this.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494124&amp;1=default&amp;2=en&amp;3=" token="kpEnsmWAMvV3sNGoGi3fbvmHePgKARfbgLpz8dZOCqc"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">abadidea (not verified)</span> on 11 Mar 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494124">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494125" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1300828213"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>The cited paper mentions "heritable damage responses." Is damage restricted to random acts of nature, or can there be such a thing as self damage for some unknown purpose that will nevertheless be heritable?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494125&amp;1=default&amp;2=en&amp;3=" token="r3XGYgCl0Xtyh9E_8WnbwyrIfi0qPeSP_W4A8P9nPe0"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Barry (not verified)</span> on 22 Mar 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494125">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494126" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304258046"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Do the cells that retain this memory of an experience then pass on that memory to those they have been divided into. Inheritance of acquired memories of experience perhaps? And how many generations does this affect? And can the effects of this experience ever be completely erased from the genome if the experience itself is replicated or repeated in a particular environment? And is this perhaps one of the ways that cells evolve to anticipate and deal strategically with a multitude of problems?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494126&amp;1=default&amp;2=en&amp;3=" token="G6gR_2hvfr_cYuhaHhzV-dkbnOct0b93tJ_Ax7BgBGU"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">royniles (not verified)</span> on 01 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494126">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494127" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304332847"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I see two people have left interesting questions here, but there have been no interesting answers. Are such questions then to be treated as rhetorical?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494127&amp;1=default&amp;2=en&amp;3=" token="P-_BW43OeSeEpKk8hJ-PppxcoM7N2XdMwY8ey6TzYhY"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">baron (not verified)</span> on 02 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494127">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494128" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304432153"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>hello commenters! this is devin burrill, the first author on the paper, "synthetic circuit identifies subpopulations with sustained memory of DNA damage." christina has notified me that she's been getting a lot of questions, and so we have decided to write a short blog post that answers all of these questions. keep a look out for it later this week here on christina's' blog! and thank you for all of the interest!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494128&amp;1=default&amp;2=en&amp;3=" token="f0zSlCMXxNTMbLS3aLP_Jb6DQOqAw8czRHeT69hBRZQ"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">devin burrill (not verified)</span> on 03 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494128">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494129" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1327099824"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>A very interesting article, I haven't finished reading but I can't help speculate how this work can be generalized. There are some specific carcinogenic models where p53 signaling is not activated however carcinogenesis still continues, in those models DNA-damage does however accumulate. So I wonder if the DNA-damage sensing part of this can be used to label those cells and then their continuing generations will still have the color expressed. Does that sound plausible?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494129&amp;1=default&amp;2=en&amp;3=" token="04moWvjiUL7qthGvcvC8s8WKXsEcaw8CbxtPaKrp_bw"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dhillonv10 (not verified)</span> on 20 Jan 2012 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494129">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/03/11/making-cellular-memories%23comment-form">Log in</a> to post comments</li></ul> Fri, 11 Mar 2011 14:21:24 +0000 cagapakis 146961 at https://scienceblogs.com Energy, Armpits, and Octopodes https://scienceblogs.com/oscillator/2011/02/12/energy-armpits-and-octopodes <span>Energy, Armpits, and Octopodes</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>I had a great conversation with Maggie Koerth-Baker from <a href="http://boingboing.net/sci/">BoingBoing</a> for bloggingheads.tv Science Saturday. We talked about all sorts of sciency stuff, including her upcoming book on the challenges of renewable energy, synthetic biology, the similarities between cheese and the human body, women in science/blogging, and octopus brains. I had a lot of fun chatting with Maggie and I learned a lot, and I hope you will too!</p> <p></p><center><embed type="application/x-shockwave-flash" src="http://static.bloggingheads.tv/ramon/_live/players/player_v5.2-licensed.swf" flashvars="diavlogid=34195&amp;file=http://bloggingheads.tv/diavlogs/liveplayer-playlist-ramon/34195/00:00/66:11&amp;config=http://static.bloggingheads.tv/ramon/_live/files/offsite_config.xml&amp;topics=false" height="288" width="380" allowscriptaccess="always" id="bhtv34195" name="bhtv34195"></embed></center><br /></div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Sat, 02/12/2011 - 04:16</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/bioenergy" hreflang="en">bioenergy</a></div> <div class="field--item"><a href="/tag/environment" hreflang="en">environment</a></div> <div class="field--item"><a href="/tag/food-0" hreflang="en">food</a></div> <div class="field--item"><a href="/tag/future" hreflang="en">future</a></div> <div class="field--item"><a href="/tag/gender" hreflang="en">gender</a></div> <div class="field--item"><a href="/tag/scientists" hreflang="en">Scientists</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> <div class="field--item"><a href="/tag/video" hreflang="en">Video</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2494105" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297531896"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>im in love &lt;3</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494105&amp;1=default&amp;2=en&amp;3=" token="lCXbDYT97NQ93t0jlo_TQQqcF5siUGfz2tWwVV7-p4s"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Alt (not verified)</span> on 12 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494105">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494106" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1298475489"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>As an engineering school grad, I'll add my two cents. In general, engineering is all about coming up with standards, which, once determined, will stand for a long time to come. So since, in professional work, there's always a lot of pressure for direct performance, anything that could add new complications is always met with, um, let's say a harsh and pained response. It definitely takes a mental toll over time. We'd be a better world if people were more honest about how we're changed by our personal experiences.</p> <p>Also, the best response to arguments about capability in terms of gender or race or any other split is the statistical one. For almost any study out there, the difference between group capability is dwarfed (dwarved?) by the variance within each group. Just about everyone is in the overlap. As such, the case that some inherent differences should lead to wide gaps in results doesn't have a leg to stand on, even without taking any of the strong cultural biases into account. There are almost certainly some sorts of differences due to biology, if only b/c it's hard to see any kind of difference being completely isolated, but we've clearly already shown that anything that's there has no significant affect on making a prediction for any given individual. If we can't make that kind of decision, then what exactly are we looking for? Going for the belief-neutral response always makes counter-arguments sound like the biased tripe they are.</p> <p>Keep doing good (and very cool) work!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494106&amp;1=default&amp;2=en&amp;3=" token="GjMM4eD8yqPJRc2Eyt9HMz5e7YOdUSGlqDx5GshJqso"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Rob (not verified)</span> on 23 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494106">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/02/12/energy-armpits-and-octopodes%23comment-form">Log in</a> to post comments</li></ul> Sat, 12 Feb 2011 09:16:05 +0000 cagapakis 146957 at https://scienceblogs.com Designer Bacteria https://scienceblogs.com/oscillator/2011/02/11/designer-bacteria <span>Designer Bacteria</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Synthetic biologists work on designing living cells, but engineered bacteria don't usually come up when you think of "designer" things. This year however, a synthetic biology design is up for a <a href="http://www.designsoftheyear.com/2011/01/17/nominations-announced-2/">Brit Insurance Design of the Year</a> award, up against the Lanvin Spring collection, Angry Birds, and Rock Band 3! Designers <a href="http://www.daisyginsberg.com/">Daisy Ginsberg</a> and <a href="http://www.james-king.net/">James King</a> worked in collaboration with the <a href="http://2009.igem.org/Team:Cambridge">2009 Cambridge iGEM team</a> (including awesome blogger <a href="http://labrat.fieldofscience.com/2011/02/coloured-bacteria-vs-angry-birds.html">Lab Rat</a>) to imagine ways that people could use bacteria engineered to produce pigments in the future. Check out their video about the science and design of E. chromi:</p> <iframe src="http://player.vimeo.com/video/19759432" width="510" height="325" frameborder="0"></iframe></div> <span><a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a></span> <span>Fri, 02/11/2011 - 02:42</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/art" hreflang="en">Art</a></div> <div class="field--item"><a href="/tag/bacteria" hreflang="en">bacteria</a></div> <div class="field--item"><a href="/tag/design" hreflang="en">design</a></div> <div class="field--item"><a href="/tag/friends" hreflang="en">friends</a></div> <div class="field--item"><a href="/tag/future" hreflang="en">future</a></div> <div class="field--item"><a href="/tag/igem" hreflang="en">iGEM</a></div> <div class="field--item"><a href="/tag/synthetic-aesthetics" hreflang="en">synthetic aesthetics</a></div> <div class="field--item"><a href="/tag/video" hreflang="en">Video</a></div> <div class="field--item"><a href="/tag/synthetic-biology" hreflang="en">synthetic biology</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2494098" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297413618"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Interesting... Unfortunately, the eejits will scream "IT'S UNNATURAL! ONLY DOG IS ALLOWED TO DO THAT SORT OF THING!" and completely present things out of context, while misrepresenting the facts.<br /> Fortunately, this is in Britain, so there may not be actual death threats against participants (sigh).</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494098&amp;1=default&amp;2=en&amp;3=" token="1-PTsgyAnh8HftZIsEZA_sWtiyB1gew-L-BL1CzGCm8"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Birger Johansson (not verified)</span> on 11 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494098">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494099" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297419105"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>So far have received no death threats! </p> <p>Also no one has asked me to make any dogs go purple...</p> <p>Purple bacteria are, in my opinion, slightly *more* natural than mobile-phone games, which is the competition that we are up against...</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494099&amp;1=default&amp;2=en&amp;3=" token="G9mQTTMzmSGvRSpPYFr_UtrNkFXlLPvYBtvq9NF7CQE"></drupal-render-placeholder> </div> <footer> <em>By <a rel="nofollow" href="http://labrat.fieldofscience.com/" lang="" typeof="schema:Person" property="schema:name" datatype="">Lab Rat (not verified)</a> on 11 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494099">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494100" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297441054"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>I'd love to see this, but the graphic doesn't open as a video for me. Is it being blocked by AdBlocker or something?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494100&amp;1=default&amp;2=en&amp;3=" token="GT5k1XQvrOwy6zdZ41iw-Oppz1iMCEV8EjpN1TPRnJ0"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">NoniMausa (not verified)</span> on 11 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494100">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="307" id="comment-2494101" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297499505"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Here's the direct link to vimeo in case the embedded video isn't working for you: <a href="http://vimeo.com/19759432">http://vimeo.com/19759432</a></p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494101&amp;1=default&amp;2=en&amp;3=" token="IPoIqo9uDNfusR12N9hfWqmTbWdUoXrMwH5-q1x6L_Y"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a> on 12 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494101">#permalink</a></em> <article typeof="schema:Person" about="/author/cagapakis"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/cagapakis" hreflang="en"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494102" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297534976"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Orange Liberation Front? Really? I guess I don't understand the second half of the video. I'm totally down with chromatic engineering of bacteria (seems like you a "You had me at hello" sort of situation), but I'm not sure why the timeline with the fantastical speculations is necessary.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494102&amp;1=default&amp;2=en&amp;3=" token="S9LMaUUsl5EhWrfAtMnyulN9pfnSq_ovhJeY3timdo0"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dwayne stephenson (not verified)</span> on 12 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494102">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="307" id="comment-2494103" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1297579126"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>A lot of those crazy ideas in the timeline (I think) were ideas that the iGEM students came up with during a workshop designed to make them think creatively about future implications of their work. It's easier to understand the possible short-term uses but difficult to imagine what the future will be like. Some of them can get silly perhaps, but it's a great exercise for any student and biological engineer.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494103&amp;1=default&amp;2=en&amp;3=" token="9v9H40JwYyFZcWPBS-UW40Q-Y4aHGjcN5Ng7sknZJAI"></drupal-render-placeholder> </div> <footer> <em>By <a title="View user profile." href="/author/cagapakis" lang="" about="/author/cagapakis" typeof="schema:Person" property="schema:name" datatype="">cagapakis</a> on 13 Feb 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494103">#permalink</a></em> <article typeof="schema:Person" about="/author/cagapakis"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/author/cagapakis" hreflang="en"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2494104" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1304267310"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>can you guys make some retroviruses that implant glow in the dark or UV reactive pigment sequences into my dermal cells, please. that'd be cool. and i'm jealous. when i was at cambridge we weren't writing bio code.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2494104&amp;1=default&amp;2=en&amp;3=" token="1Qga4I5k338TGvuOiijJjU3H-KuyyRe2oS7rrBxefps"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">flow in (not verified)</span> on 01 May 2011 <a href="https://scienceblogs.com/taxonomy/term/17358/feed#comment-2494104">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/oscillator/2011/02/11/designer-bacteria%23comment-form">Log in</a> to post comments</li></ul> Fri, 11 Feb 2011 07:42:24 +0000 cagapakis 146956 at https://scienceblogs.com