Chemistry https://mag.uchicago.edu/tags/chemistry en Light hearted https://mag.uchicago.edu/science-medicine/light-hearted <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1908_Searcy_Lighthearted_header_0.jpg" width="2000" height="1000" alt="Illuminated heart illustration." typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" about="/profile/mrsearcy" typeof="schema:Person" property="schema:name" datatype="">mrsearcy</span></span> <span>Wed, 08/21/2019 - 13:59</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item"><p>(iStock.com/magicmine)</p> </div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/maureen-searcy"> <a href="/author/maureen-searcy"> <div class="field field--name-name field--type-string field--label-hidden field--item">Maureen Searcy</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/inquiry" hreflang="en">Inquiry</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item">09.03.2019</div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item"><p>Chemist Bozhi Tian illuminates pacemaker technology.</p> </div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Sometimes the heart needs a hand, like when it beats too quickly, too slowly, or out of sync.</p> <p>Our hearts have an innate electrical system that controls their rhythm, and when that system malfunctions, physicians may opt for a pacemaker. This matchbox-sized device consists of a battery, a computerized generator, and electrodes that attach to the heart. When the pacemaker detects an abnormality, it sends a little burst of electricity to get the heartbeat back on track.</p> <p>Traditional pacemakers, first used in humans in 1958, come with inherent risks. They’re “not freestanding,” explains associate professor of chemistry <a href="http://tianlab.uchicago.edu" target="_blank"><strong>Bozhi Tian</strong></a>. The need for a battery pack increases the device’s size, “making implantation a more invasive procedure.”</p> <p>The size also causes irritation, which can lead to an inflammatory response. The device can get coated with immune cells and fibrous material from the extracellular matrix—the network of proteins and carbohydrates found in the space between cells. This type of biofouling, Tian says, “reduces the pacemaker’s electrical signal transduction efficiency because signals will get lost.”</p> <p>His team has developed a potential solution: a wireless pacemaker powered by light. The device is based on existing solar cell technology, but shrunk down to the nanoscale—a mesh of silicon nanowires embedded in polymer for support.</p> <div class="story-inline-img"> <figure role="group"><img alt="Close up of pacemaker mesh." data-entity-type="file" data-entity-uuid="ecf8057f-e274-442b-8f77-336223c6a443" src="/sites/default/files/inline-images/1908_Searcy_Lighthearted_A.jpg" /><figcaption>An optical microscopy image of the silicon nanowire mesh shows high-density random nanowires supported over a polymer framework. (The density increases contact area between the wires and the heart muscle cells; the random configuration is easier to manufacture.) (Image courtesy Bozhi Tian)</figcaption></figure></div> <p>Silicon, a semiconductor that serves as a building block for computer chips, is an ideal material because it has “a lot of electronic and optical functions you can play with,” says Tian. “You can convert light energy into electricity.”</p> <p>Working with both cultured cells in a dish and isolated rat hearts, Tian’s team attached the mesh to heart muscle tissue and then scanned the mesh-coated area with a laser, delivering pulses of light. The mesh in turn produced electricity, activating the heart cells to beat at the same frequency as the flashes. Scanning, rather than the direct application of light, is more efficient and safer for the cells, which can be damaged by too much energy.</p> <p>While traditional pacemaker surgery is considered minimally invasive, with the device implanted through a small incision in the chest, Tian’s mesh could be delivered even less invasively, via needle injection. The surgeon would even target areas of the heart with pacemaker cells, mostly found in the sinoatrial node close to the right atrium wall. These cells naturally generate electrical impulses, and that energy flows throughout the heart, causing it to pump.</p> <p>Light could be delivered in a few different ways, including through an optical fiber. After injecting the mesh, a fiber about the diameter of a human hair could be plugged into the same hole, with one end touching the mesh and the other exposed to the outside world, able to guide light to the pacemaker.</p> <p>Traditional pacemakers can be permanent or temporary. If an irregular heartbeat is caused by something acute and reversible, such as drug toxicity or infection, a pacemaker may be needed only until the underlying problem is solved, and this is the type Tian’s light-powered mesh is aimed at replacing.</p> <p>Nanostructure silicon can dissolve inside a human body within a few weeks, making it optimal for transient applications. (Silicon degrades into silicic acid, which can be filtered by the kidneys, so in small enough doses, it’s safe for humans. The polymer support for the silicon can be biodegradable as well.) “You would inject one dosage, apply the light pulses, and then treat the patient for a short window, perhaps a few days,” says Tian. “Then there’s no need for additional surgery” to remove the device.</p> <p>Much of the work in Tian’s lab has the potential to directly improve medical care. This project builds on technology originally developed to stimulate neurons, a concept pioneered by <a href="https://biophysics.uchicago.edu/the-students/ramya_parameswaran/" target="_blank"><strong>Ramya Parameswaran</strong></a>, PhD’18, an MD/PhD student who completed her biophysics degree in Tian’s lab and is now finishing her medical training at the Pritzker School of Medicine.</p> <p>“At this stage we certainly hope to work with medical doctors because that’s how we make real impact,” says Tian, “but we must first optimize the technology,” improving the device’s optical pacing, efficiency, and power demands. Tian predicts they might be ready to approach clinicians in a couple of years—if they keep up this pace.</p> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/physical-sciences-division" hreflang="en">Physical Sciences Division</a></div> </div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/light-hearted" data-a2a-title="Light hearted"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Flight-hearted&amp;title=Light%20hearted"></a></span> Wed, 21 Aug 2019 18:59:44 +0000 mrsearcy 7169 at https://mag.uchicago.edu The other one https://mag.uchicago.edu/science-medicine/other-one <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1708_Searcy_Other-one.jpg" width="725" height="396" alt="The Butler sisters" title="The Butler sisters" typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" about="/profile/jmiller" typeof="schema:Person" property="schema:name" datatype="">jmiller</span></span> <span>Tue, 08/08/2017 - 09:08</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item"><p>Laurie (left) and Lynne (right) at Botany Pond during one of Lynne’s frequent visits. (Photography by Nathan Keay)</p> </div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/maureen-searcy"> <a href="/author/maureen-searcy"> <div class="field field--name-name field--type-string field--label-hidden field--item">Maureen Searcy</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/core" hreflang="en">The Core</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item">Summer/17</div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item"><p>Twins Laurie and Lynne Butler—one a UChicago chemistry professor, the other a double alumna—discuss math, horses, and a college boyfriend who never got them confused.</p> </div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Laurie Butler earned a BS in chemistry from MIT and a PhD from UC Berkeley before joining the University of Chicago chemistry faculty. Her twin sister, Lynne Butler, AB’81, SM’13, earned a PhD from MIT before joining Princeton’s math faculty. She’s now a professor at Haverford College. Lynne returned to UChicago for a master’s in statistics “just for fun.” Laurie’s husband, Michael Stein, is a statistician at UChicago who started out in math.</p> <p>The <em>Core</em> caught up with the sisters during one of their frequent—at times weekly—visits to see each other. Interview has been edited and adapted.</p> <hr /><h2><strong>Was there a shared experience that led you both to STEM (science, technology, engineering, and math) fields?</strong></h2> <p><strong>Lynne: </strong>There was quite a gap between our four older siblings and the two of us. The boys, the girls, and the twins is how we usually say it. The oldest is 10 years older than me. The next is nine, next is eight, next is six, and then Laurie is four minutes older. When those four were in college, they would come back to Garden City for a visit—on Long Island where we lived at the time—and teach us stuff. I remember, even when they were in high school—especially my sister Debbie, who now lives in Africa, and my brother Bruce—they’d teach us cube roots when we were learning square roots.</p> <p><strong>Laurie: </strong>I always thought you had to be a medical doctor to do research, but our sister Sharon went to New College of Florida and taught us what a PhD was.</p> <div class="story-inline-img"> <figure role="group"><img alt="Dressing alike" data-entity-type="file" data-entity-uuid="3ecb1c3d-77a4-45b2-ae61-a5c37f23493d" src="/sites/default/files/inline-images/1708_Searcy_Other-one_spotA.gif" /><figcaption>The Butler twins were dressed alike until high school. In this photo they were not sure which one was which; their brother Sean confirmed Laurie is on the left. (Photo courtesy Laurie Butler)</figcaption></figure></div> <h2><strong>So all of the siblings were focused on education?</strong></h2> <p><strong>Lynne: </strong>The top four were not education oriented.</p> <p><strong>Laurie: </strong>Sharon was eventually.</p> <p><strong>Lynne: </strong>She was the second time around. When my father wrote his will, he left money for Laurie’s and my education but not for further education for the other siblings. He was mad at them for wasting their college opportunity.</p> <p><strong>Laurie: </strong>I didn’t know that. Our mother was a nurse, and our father was a doctor. Dad used to say, “You’ll never get a job in humanities.” He was worried about making a living, but he loved literature. He wrote a novel himself and used to pick on our older siblings, saying that Robert Louis Stevenson wrote this poem when he was 14, and what have they done?</p> <p><strong>Lynne: </strong>He was born in 1908, so he experienced the Depression. That stayed with him. And my mother came from a farming family—raised by her grandparents in upstate New York.</p> <h2><strong>Lynne, what got you interested in math? Laurie, why chemistry?</strong></h2> <p><strong>Laurie: </strong>Probably that high-school math teacher. We went to high school in St. Petersburg, Florida, where we moved after our father had a stroke and the family needed to save some money.</p> <p><strong>Lynne: </strong>Yeah, Mr. Mead, who studied with me. He wanted to learn group theory, and so did I, so we learned together.</p> <p><strong>Laurie:</strong> But when he was teaching linear algebra, I was like, I don’t care. I don’t get this. Now I love linear algebra. But something about how he taught it.</p> <p><strong>Lynne: </strong>He taught linear algebra as a pure math subject rather than its incredibly rich, important applications. I was fine with that at the time, but now I see how for the vast majority of students, that was the wrong approach. He alienated my dearest sister! Otherwise we might have been mathematicians together.</p> <p><strong>Laurie: </strong>I went to Johns Hopkins for one year before MIT, and I remember trying to pick what science to do. I was going to major in molecular biology and thought neuroscience would be cool. At the library I opened an issue of the <em>Journal of Neuroscience</em>. I read the experimental section of the first article, and it started with, “We used the heads of a thousand cats.” [Slaps hands together.] I’m out of there! So I switched to chemistry.</p> <p><strong>Lynne: </strong>Laurie’s loved animals from when she was really little.</p> <div class="story-inline-img"> <figure role="group"><img alt="The Butler sisters in high school" data-entity-type="file" data-entity-uuid="a09824f0-4aef-4f90-8659-bda3b6ead2a0" src="/sites/default/files/inline-images/1708_Searcy_Other-one_spotB.gif" /><figcaption>During high school, Laurie (left) wore pants and Lynne (right) wrote dresses, but their classmates and teachers couldn’t remember which one wore what. (Photo courtesy Laurie Butler)</figcaption></figure></div> <h2><strong>You have UChicago and MIT in common, though at different times. Did you choose your postcollege paths because of the other’s experience?</strong></h2> <p><strong>Lynne: </strong>Both of us knew from the very beginning that we would have to take our best offer at every decision point to be successful. But there was something fun that happened—</p> <p><strong>Laurie: </strong>The MIT transition.</p> <p><strong>Lynne:</strong> I was about to start at MIT and Laurie was finishing there, heading off to Berkeley. So people saw her in the spring and me in the fall. A lot of people said hello to me that I didn’t know.</p> <p><strong>Laurie: </strong>They were wondering why I was spending a fifth year at MIT.</p> <h2><strong>Did you play along?</strong></h2> <p><strong>Lynne: </strong>There’s what they call the Infinite Corridor at MIT. Once, I was about a quarter of the way down, and someone was coming from the other direction, and we were still quite distant, maybe 40 yards apart. He was looking at me, so I knew it was coming. I preemptively said, “I’m actually not Laurie, I’m Lynne, her twin sister.” The guy did not know Laurie—was totally mystified why I was launching into this explanation.</p> <p><strong>Laurie: </strong>But when I visit Haverford, where everyone stops to chat, I just walk right by. I’m a little quiet.</p> <p><strong>Lynne: </strong>People would come to me the next day and say, “Lynne, did I say something wrong?” Oh no, Laurie’s visiting.</p> <div class="story-inline-img"> <figure role="group"><img alt="Lynne's wedding" data-entity-type="file" data-entity-uuid="fed06c0d-7e2d-4bc4-a467-e3284a35ee2c" src="/sites/default/files/inline-images/1708_Searcy_Other-one_spotC.jpg" /><figcaption>Lynne (left) at her wedding to Miller Maley, a computer scientist; Laurie (right) with husband Michael Stein, the Ralph and Mary Otis Isham Professor in Statistics. (Photo courtesy Laurie Butler)</figcaption></figure></div> <h2><strong>Can you describe your specific work?</strong></h2> <p><strong>Lynne: </strong>I was first interested in topology, but there was quite a bit of sexism in that field. My first graduate dissertation adviser at MIT was an algebraic topologist, who the other graduate student women warned me against. He would ask, “Do you plan to get married? Do you plan to have children?” And if you said yes, he’d say, “Then you shouldn’t be in mathematics.”</p> <p><strong>Laurie: </strong>But the guys could have children.</p> <p><strong>Lynne: </strong>At that point in my life, I didn’t want children, and I wasn’t interested in getting married, so I felt like it would be fine. That was a mistake. Our relationship really deteriorated when, during one of our 6 a.m. meetings—which is when he insisted on meeting me every morning—I commented on a stack of papers on his desk. I thought it must be his most recent publication and was hoping that if I mentioned it, he would offer me one. Instead he reported me to the chair for “intruding on his space.” The guy was really odd. But because there were only three topologists, he would be asked about me when I applied for jobs whether or not I was his student. The chair told me, “You can’t stay in topology.” So I switched to combinatorics and loved it.</p> <h2><strong>Sorry, combina-what?</strong></h2> <p><strong>Lynne: </strong>Combinatorics. Counting. When you’re a student in grade school, you count subsets of a set. For my thesis, I counted subgroups of a group. It was algebraic combinatorics—the algebra came from group theory and the combinatorics came from the counting. It was a very hot field at the time. My original adviser’s students were getting jobs in North Dakota. My first job was at Princeton.</p> <p><strong>Laurie:</strong> It was like getting into nanomaterials 20 years ago.</p> <p><strong>Lynne: </strong>But after 20 years I got bored. I taught a freshman class that was half calculus and half probability theory, and women did much better on the application material. I thought, if I want to attract women to STEM, I should learn statistics. At Princeton I was the only woman out of 56 math faculty members. So this is a driver for me.</p> <p><strong>Laurie: </strong>They used to give her photocopying in the elevator because they thought she was a secretary. I had it easier. Well, there was one sexist thing. I wanted to work with Yuan Lee; he had not yet won the Nobel Prize, and he was on faculty at Berkeley. When I visited the Lee group, it was a friendly crowd. I was still an MIT undergrad, so I was used to a largely male crowd. The students took me out for pizza, and one physicist in the group said, “The Lee group is no place for women.” But Yuan was really great.</p> <p>I did photodissociation experiments—dissociating molecules by letting them absorb light and trying to understand what products they make. And then I moved to Chicago and fretted about breakdown of the Born-Oppenheimer approximation—the assertion that nuclear and electronic motion can be separated.</p> <p><strong>Lynne:</strong> Laurie’s work on the Born-Oppenheimer approximation was quite groundbreaking, and the chemists at my little college knew about it. So I get some mileage at my school for having a famous twin.</p> <p><strong>Laurie: </strong>We get to use the other one as collateral. When theoretical physical chemists say they’re better than experimentalists, I can say, well, my sister’s a pure mathematician.</p> <p><strong>Lynne:</strong> If anyone had any prejudices, we would be able to defeat them right off the bat. They’d say to me, you’re a Princeton mathematician—you can’t have children. And I can say, my twin sister has a child, and she’s at the University of Chicago.</p> <p><strong>Laurie: </strong>Of course Mike did most of the work. My husband and I were married a long time before we decided to have a kid. We got married when I was 24, and I was 34 before I got pregnant. We had never really talked about having kids, but Mike’s a statistician, so he was slowly working on me, saying things like, “Surveys show that people say the best time of their lives was when their kids were little.” So finally I got the hint. So I said, if I take care of the first nine months, for obvious reasons, and you take care of the next nine years, I’m with you. He didn’t quite agree to that; he said I ought to be involved. But he was a really good parent. He’s since given talks to women scientists, and he tells them that they’ve got to marry the right guy.</p> <p><strong>Lynne: </strong>To be successful, I think that’s right. I always tell people that I don’t have to have children because genetically, Laurie’s daughter, Ellyn [Butler, LAB’13], is just as much mine as hers.</p> <p><strong>Laurie: </strong>And Ellyn pointed out maybe more because of mutations.</p> <h2><strong>Laurie’s colleague Chuan He has said about his work on epigenetics that DNA sequence accounts for only so much of who you are, that environment can change your genetics. Does that affect your identity as twins—that you might not actually be identical at the molecular level?</strong></h2> <p><strong>Lynne: </strong>Well, you’re moving through your early years in exactly the same environment. People don’t bother distinguishing you for quite a long time.</p> <p><strong>Laurie: </strong>Like our father. He was very busy, so we were just “the twins.”</p> <p><strong>Lynne: </strong>We intentionally diverged in high school and were already quite different, but people were still confusing us. I wore dresses and Laurie wore pants, but people forgot which one wore what. We deliberately went to different colleges. We missed each other terribly but wanted people to know us as separate individuals.</p> <p><strong>Laurie: </strong>What did that one clerk ask us? How do you know that you’re Laurie? I used to fool my classes.</p> <p>There are a few things in physical chemistry that are math-y, so once in a while when Lynne was visiting I’d send her in to lecture. And then I’d walk in. I told them it’s really important when you are a young professor to be able to work double time.</p> <p><strong>Lynne:</strong> We also tried to fool my boyfriend when I was in college here. We had him sit on a couch, the two of us were behind him, and randomly one or the other of us would reach forward and shake his hand. Every single time he guessed correctly. I asked how, and he said, “You squeeze back.”</p> <p><strong>Laurie: </strong>She has a very unusual husband now. Miller [Maley] went to college at 12 and had one of his two PhDs by the time he was 20.</p> <p><strong>Lynne: </strong>As the only woman on Princeton’s math faculty, I had my pick! But I picked him from computer science.</p> <h2><strong>Laurie, you’re working part time now and planning a move. What prompted that change?</strong></h2> <p><strong>Laurie: </strong>Six years ago I had bilateral breast cancer. It made me think carefully about the amount of time I was spending at work versus with family. So reducing my workload meant I could take my daughter to flute auditions at different colleges. Mike would normally shoulder that sort of thing. It also reminded me of a promise to myself to move east.</p> <p>That’s when I decided to move in with Lynne. It’s hard because I’ve been ready to go for a long time, but Mike’s also a faculty member here and master of the Physical Sciences Collegiate Division. And we’d have lost an enormous amount of tuition benefit for our daughter. So we made a deal that when I turned 59, I would be there [at Lynne’s home in New Jersey]. Mike has a sabbatical in 2018–19, so I’m moving in one year, and Mike will come a couple of months later.</p> <p><strong>Lynne: </strong>They’re not promising to stay forever—just for a year to see how they like it. I plan way ahead. When we bought our house in 1997, I was looking for a place with a first-floor master bedroom because I knew I wanted to die in that house—</p> <p><strong>Laurie: </strong>She likes talking about dying in that house.</p> <p><strong>Lynne: </strong>We got a very large house. Even though it’s just me, my husband, and our brother who lives in the basement, I knew I wanted Laurie and her husband to move in with me eventually. I’m glad it’s finally happening.</p> <p><strong>Laurie: </strong>You haven’t let me forget it! She planted the seed and then nurtured it!</p> <h2><strong>You’re already showing your home. Where will you stay if it sells quickly?</strong></h2> <p><strong>Laurie: </strong>We have a place in Crete, Illinois, a tiny town next to Beecher where our two horses are. We’ve been walking to work and driving to the horses on the weekend; we would reverse that.<br />  <br /> [Laurie pulls up a photo of the two of them with her horse Colors.]</p> <div class="story-inline-img"> <figure role="group"><img alt="The Butler sisters with Colors, Laurie's horse" data-entity-type="file" data-entity-uuid="68a08892-ceac-4ffb-b1a0-1488167144a9" src="/sites/default/files/inline-images/1708_Searcy_Other-one_spotD.gif" /><figcaption>Lynne (left) and Laurie (right) with Laurie’s horse Colors (center). (Photo courtesy Laurie Butler)</figcaption></figure></div> <p><strong>Lynne: </strong>She’s a descendant of Northern Dancer.</p> <p><strong>Laurie: </strong>She was bred to be a racer in Kentucky but had an accident early on. The other one is Lucky. He’s a real snot.</p> <h2><strong>You’re taking veterinary technician classes now, right Laurie?</strong></h2> <p><strong>Laurie: </strong>Yes, at a little college near Lynne. They have a practicum at the New Bolton Center, where racehorses are treated. That’s what attracted me to the program.</p> <h2><strong>Do you want to get a job in vet tech? Or is this for retirement?</strong></h2> <p><strong>Lynne: </strong>Laurie wants to work with horses; she doesn’t care whether or not she gets paid. She also likes being a student again.</p> <p><strong>Laurie: </strong>It’s time to do good deeds.</p> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> <div class="field--item"><a href="/tags/mathematics" hreflang="en">Mathematics</a></div> <div class="field--item"><a href="/tags/twins" hreflang="en">Twins</a></div> <div class="field--item"><a href="/tags/family" hreflang="en">Family</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/college-alumni" hreflang="en">College alumni</a></div> </div> <div class="field field--name-field-refformats field--type-entity-reference field--label-hidden field--item"><a href="/formats/interview" hreflang="en">Interview</a></div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/other-one" data-a2a-title="The other one"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Fother-one&amp;title=The%20other%20one"></a></span> Tue, 08 Aug 2017 14:08:42 +0000 jmiller 6646 at https://mag.uchicago.edu Making a mark https://mag.uchicago.edu/science-medicine/making-mark <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1511_Searcy_Making-mark.jpg" width="1600" height="743" alt="" typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" about="/profile/mrsearcy" typeof="schema:Person" property="schema:name" datatype="">mrsearcy</span></span> <span>Thu, 11/19/2015 - 19:27</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item"><p>Epigenetics provides an additional genetic coding process, expanding complexity exponentially. (Photography by Peter Barreras, Howard Hughes Medical Institute)     <img src="http://mag.uchicago.edu/sites/default/files/2015_Fall_Inquiry-cover.jpg" width="140" /></p> <h5>This article originally appeared in the Fall 2015 issue of <em>Inquiry</em>, the biannual publication produced for University of Chicago Physical Sciences Division alumni and friends.</h5> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="../inquiry-archive" target="_self">VIEW ALL <em>INQUIRY</em> STORIES</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://mag.uchicago.edu/sites/default/files/Inquiry_Fall-2015.pdf">DOWNLOAD THE LATEST ISSUE (PDF)</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://physical-sciences.uchicago.edu/news/archive" target="_blank">READ ADDITIONAL PSD NEWS</a></div> </div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/maureen-searcy"> <a href="/author/maureen-searcy"> <div class="field field--name-name field--type-string field--label-hidden field--item">Maureen Searcy</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/inquiry" hreflang="en">Inquiry</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item">Fall/15</div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item"><p>Chuan He breaks new ground in RNA and DNA epigenetics.</p> </div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Three billion—the number of base pairs in the human genome—sounds like a huge number. But of those billions of bases, humans appear to have only about <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204768/" target="_blank">19,000 protein-coding genes</a>. And while that may sound like a large number as well, those genes alone can’t account for the vast complexity of a human being with trillions of cells, all with their own identities.</p> <p>The standard flow of information coded into DNA, transcribed into RNA, and translated into protein provides too small a genetic template to accommodate the diversity of living systems. This discrepancy can be explained in part by <a href="http://www.britannica.com/science/epigenetics" target="_blank">epigenetics</a>: changes to gene expression that don’t change the underlying DNA sequence.</p> <p>Epigenetics “is basically a coding process,” says <a href="https://chemistry.uchicago.edu/faculty/faculty/person/member/chuan-he.html" target="_blank">Chuan He</a>, the John T. Wilson Distinguished Service Professor in Chemistry. The DNA sequence is a predetermined template, but one with hundreds of millions of spots that can accept chemical flags that alter gene expression. One such template modification is <a href="http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070" target="_blank">methylation</a>.</p> <p>Three classes of proteins carry out epigenetic coding: “writer” enzymes that apply tags or marks, “eraser” enzymes that remove the marks, and “reader” proteins that recognize and bind to the marks. This tagging provides an additional genetic coding process, expanding complexity exponentially, and explains, for instance, how cells with identical genome sequences can develop into different cell types. A deeper understanding of epigenetics provides insight into essentially all life on earth.</p> <p> <h5>[[{"type":"media","view_mode":"media_original","fid":"3161","attributes":{"alt":"","class":"media-image","height":"162","typeof":"foaf:Image","width":"500"}}]] The methylation on messenger RNA that He’s team discovered is reversible, which could affect a range of properties and functions that play essential roles in medical and biological research. (Image courtesy Chuan He)</h5> </p> <p>For almost half a century, geneticists have studied DNA methylation. For about three decades, they have been studying the same type of modifications on histones—the proteins around which DNA coils. But until recently, partly for practical and partly for conceptual reasons, no one considered the role RNA might play in epigenetics.</p> <p>“In the beginning, it was easier to study DNA and histones,” says He. “They're much more stable. You can isolate them and perform various analyses.” And because RNA has a shorter half-life inside cells, scientists thought it might merely be a template that transfers genetic information from DNA to protein. Yet in the past few decades, as more capable analytic sequencing technology has been invented, researchers have discovered that RNA plays major functional roles in many processes.</p> <p>He, who joined UChicago in 2002 and now directs the <a href="http://ibd.uchicago.edu/" target="_blank">Institute for Biophysical Dynamics</a> and is a <a href="http://news.uchicago.edu/article/2013/05/09/chuan-he-named-howard-hughes-medical-institute-investigator" target="_blank">Howard Hughes Medical Institute Investigator</a>, came to study RNA via the scenic route. A synthetic chemist who had worked in organic synthesis, he also studied biochemistry; investigated pathogenic bacteria with <a href="https://biomedsciences.uchicago.edu/page/olaf-schneewind-md-phd" target="_blank">Olaf Schneewind</a>, the Louis Block Professor in Microbiology; and later collaborated with <a href="https://biomedsciences.uchicago.edu/page/tao-pan-phd" target="_blank">Tao Pan</a>, professor in biochemistry and molecular biology, on RNA biology.</p> <p>Researchers have long known about RNA methylation, but they believed it was a static state, playing a minor role. In 2010 He—who had been working on DNA epigenetics—discovered the first RNA demethylase, called <a href="http://news.uchicago.edu/article/2011/10/18/new-research-links-common-rna-modification-obesity" target="_blank">FTO</a>, an eraser that removes a methyl group from RNA. His discovery proved that RNA methylation is reversible and thus a dynamic modification. Publishing the research in 2011, He’s lab founded the research field of RNA epigenetics.</p> <p>He’s team went on to discover and describe the writer, eraser, and reader proteins involved in RNA methylation. Focusing particularly on the readers, which ultimately affect the cell’s biological functions, He is gaining a mechanistic understanding of the methylation pathway, with “the implication that this is going to impact most biological processes.” He suspects his lab will have a complete characterization of the reader functions in a couple of years.</p> <p>The next questions to address are how and why the erasers regulate demethylation and the writers selectively restore the mark. And in the longer term, how these proteins and pathways affect or control cell differentiation, development, and human diseases.</p> <p>While He is making waves in RNA, he hasn’t given up his DNA work. A recent revelation, in fact, links back to his field-making RNA discovery. Scientists know that the DNA base cytosine gets methylated in both multicellular and single-cell organisms alike. (Cytosine methylation is the most thoroughly researched and best understood epigenetic DNA mark.) The DNA base adenine was thought to be methylated only in bacterial cells. However, homologues of the RNA demethylase protein that He’s lab discovered remove a methyl group from adenine in multicellular organisms.</p> <p>With associate professor Laurens Mets in molecular genetics and cell biology, He set off to find <a href="http://news.uchicago.edu/article/2015/05/05/new-form-dna-modification-may-carry-inheritable-information" target="_blank">methylated DNA adenine in eukaryotes</a>, and they did—in algae, worms, and fruit flies. The discovery led to three <em><a href="http://www.cell.com/cell/abstract/S0092-8674(15)00427-4" target="_blank">Cell</a></em> papers published in April by He’s group, a team at Harvard, and a team in China. The DNA mark is also found in mammals, according to as-yet unpublished data.</p> <p>“This is a completely new mark,” says He. “This is new biology emerging.” These epigenetic pathways, involving adenine methylation in RNA and DNA in eukaryotes and mammals, play a critical role in innumerable biological processes, and He is providing vital groundwork for advances in medical and life sciences. “We’re doing the fundamental research, mapping up the players, the building blocks,” says He, “and then others can study immunology, infection, cancer therapy, diabetes, metabolism, neurogenesis, plant biology, developmental biology. You name it, these pathways are involved.”</p> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> <div class="field--item"><a href="/tags/genetics" hreflang="en">Genetics</a></div> <div class="field--item"><a href="/tags/dna" hreflang="en">DNA</a></div> <div class="field--item"><a href="/tags/rna" hreflang="en">RNA</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/physical-sciences-division" hreflang="en">Physical Sciences Division</a></div> </div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/making-mark" data-a2a-title="Making a mark"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Fmaking-mark&amp;title=Making%20a%20mark"></a></span> Fri, 20 Nov 2015 01:27:40 +0000 mrsearcy 5220 at https://mag.uchicago.edu Climate change 101—and beyond https://mag.uchicago.edu/science-medicine/climate-change-101-and-beyond <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1505_Carr_Climate-change.gif" width="700" height="325" alt="" typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" about="/profile/jmiller" typeof="schema:Person" property="schema:name" datatype="">jmiller</span></span> <span>Tue, 06/09/2015 - 16:53</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item"><p>GISS-E2-H Soil Moisture Annual Mean, 2050.</p> </div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/sean-carr-ab90"> <a href="/author/sean-carr-ab90"> <div class="field field--name-name field--type-string field--label-hidden field--item">Sean Carr, AB’90</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/inquiry" hreflang="en">Inquiry</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item">Spring/15</div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item"><p>Geophysical Sciences’ David Archer has a way with inconvenient truths.</p> </div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>U<span style="line-height: 1.538em;">ndergraduates in&nbsp;</span><a href="http://geosci.uchicago.edu/directory/david-archer" target="_blank">David Archer</a><span style="line-height: 1.538em;">’s Core class, Climate Change: Understanding the Forecast (PHSC 134), don’t have a choice: they have to do the math. The Boltzmann constant pops up early in the first lecture, on heat and light, and by the end of those first 50 minutes in Kent 107, Archer is flinging blackboards up and down to teach these students—resolutely </span><em style="line-height: 1.538em;">not</em><span style="line-height: 1.538em;"> science majors—how to convert calories into joules and joules per second into watts.&nbsp;</span></p> <p>For the more casual learners in his online course <a href="https://www.coursera.org/course/globalwarming" target="_blank">Global Warming: The Science of Climate Change</a>, launched in fall 2014 and open to anyone with a fast enough internet connection and a curiosity about climate science, Archer is more lenient. He doesn’t avoid math altogether but says, “I would hate to have you get turned off by not wanting to deal with math.” The online version also skips over quantum mechanics; otherwise the two courses cover much of the same information.&nbsp;</p> <p>A professor of <a href="http://geosci.uchicago.edu" target="_blank">geophysical sciences</a>, Archer says a course on climate change gives him an opportunity to cover more ground than he can in deep-dive graduate and undergraduate courses like Environmental Chemistry and Global Biogeochemical Cycles. “The question is informed by physics and chemistry and geology, atmospheric sciences, oceanography, energy systems, how social systems work, economics. You get to see a little bit of how all these different disciplines approach a problem, how they think, and how they work by focusing in on this fairly narrow topic.”</p> <p>The Core class and its online cousin are just two venues for Archer—whose research focuses on how ocean sedimentary processes, such as calcium carbonate dissolution and methane hydrate formation, affect atmospheric carbon dioxide—to share his work with less specialized audiences. Over the years he’s spoken at churches, atheist meetings, libraries, physics departments at other universities, retirement communities, and even Chicago’s <a href="https://www.mwrd.org/irj/portal/anonymous/Home" target="_blank">Metropolitan Water Reclamation District</a>’s Stickney wastewater treatment plant. “I’ve stopped flying places to give global warming talks,” he says. “They wanted to fly me to Iceland to give a talk at some kind of ceremonial thing. If you want me to fly there, you don’t really get what I’m trying to say.”</p> <p>And Archer does have something specific to say.</p> <p>“There’s a lot of concern in the scientific community about greenhouse gases that are very powerful but don’t last very long in the atmosphere,” he notes, giving methane as an example. Cutting methane emissions is cheaper than cutting CO<sub>2</sub>, but the methane released today has no effect on the temperature in 2040, 2050, or 2060, whereas CO<sub>2</sub>’s longevity will affect the climate that far into the future.</p> <p>“I’m what they call a CO<sub>2</sub> absolutist in the climate community,” Archer says. “I say keep your eye on the ball, and that is carbon dioxide.”</p> <p>One of the most frequent questions he gets is about Arctic methane release—“What about those big explosion marks in Siberia?” His response: “The Arctic Ocean is a tiny, tiny source of methane amidst all the rice paddies and swamps and cow farts.” If people start to believe that the natural world is doomed, “they kind of lose all interest in thinking about fighting CO<sub>2</sub> emissions.”</p> <p>Archer does envision a clear way forward. It’s not one big change. “There’s no single thing we can do today that will fix CO<sub>2</sub> emissions,” he says, “because we create CO<sub>2</sub> emissions in so many different ways.” Rather, like someone trying to lose weight, it’s several smaller changes that add up to a big difference. Those changes are known as wedges. Investing in nuclear power is a wedge. Windmills. “Cars that get 60 miles a gallon instead of 30 could be a wedge,” Archer says, “even if there were a lot more cars in the future.” &nbsp;</p> <p>When Archer explains why it’s so important to him to share this message in as many ways as he does, he sounds like a colleague teaching a humanities Core course across the quad in <a href="http://architecture.uchicago.edu/locations/cobb_lecture_hall/" target="_blank">Cobb Hall</a>.&nbsp;</p> <p>“What if the ancient Greeks had figured out fossil fuels? What if they knew what they were doing but did it anyway?” Archer asks. “You know, left the lights on for a century, just sort of frittered it away. And what if we knew today that the world we lived in was degraded because of that? What right would they have to do that? And what would we think of them?”&nbsp;</p> <p>Socratic dialogue aside, Archer knows he’s not about to be charged with corrupting UChicago’s youth. When he’s spoken to parents of <a href="http://college.uchicago.edu" target="_blank">College</a> students at <a href="https://familyweekend.uchicago.edu" target="_blank">Family Weekend</a>, he says, “They’re all, ‘Yes, teach them this.’”</p> <p>Last fall Archer took his message to the University’s <a href="http://news.uchicago.edu/multimedia/521st-convocation-university-ceremony-university-chicago" target="_blank">521st Convocation</a>, where he addressed “graduating carbon atoms” from across the University. Even with the title “<a href="https://www.youtube.com/watch?v=QcB_dCy4qNw&amp;feature=youtu.be&amp;utm_source=*+UChicago+News+-+All+Subscribers&amp;utm_campaign=e7777ae781-2014-01-08-newsletter&amp;utm_medium=email&amp;utm_term=0_4d15d79ba2-e7777ae781-153966141" target="_blank">The Great Carbon Conspiracy</a>,” his tone was lighthearted and appropriately inspiring, closing with “a special salute to the sentient carbon atoms—you know who you are. I just want to say watch out for the fossil fuel thing, that’s kind of serious. But I know you’re good for it, so that’s cool.” Here, too, he skipped the math.</p> <p><strong>Accessing&nbsp;Archer</strong></p> <p>David Archer offers two versions of his climate change course online. Visitors can learn about different topics in bite-sized portions as recorded for Archer’s massive open online course. Or they can watch an almost raw stream of PHSC 134, which includes students coughing, shuffling papers, and asking some terrific fundamental questions: “Are light and radiation the same thing?”</p> <p>Archer also offers the public the same interactive climate change models that PHSC 134 students use in labs. Visit <a href="http://climatemodels.uchicago.edu" target="_blank">climatemodels.uchicago.edu</a> to try them out.</p> <ul> <li><span style="line-height: 1.538em;"><a href="http://forecast.uchicago.edu/lectures.html" target="_blank">Archer’s climate change course</a></span></li> <li><span style="line-height: 1.538em;"><a href="http://mag.uchicago.edu/archerposts" target="_blank">Archer’s posts to&nbsp;realclimate.org</a></span></li> <li><span style="line-height: 1.538em;"><a href="http://mag.uchicago.edu/archeraddress" target="_blank">Archer’s Convocation address</a></span></li> </ul> <div> </div> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/online-learning" hreflang="en">online learning</a></div> <div class="field--item"><a href="/tags/climate-change" hreflang="en">Climate change</a></div> <div class="field--item"><a href="/tags/physics" hreflang="en">Physics</a></div> <div class="field--item"><a href="/tags/geology" hreflang="en">geology</a></div> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> <div class="field--item"><a href="/tags/atmospheric-sciences" hreflang="en">Atmospheric sciences</a></div> <div class="field--item"><a href="/tags/oceanography" hreflang="en">oceanography</a></div> <div class="field--item"><a href="/tags/energy-systems" hreflang="en">Energy systems</a></div> <div class="field--item"><a href="/tags/economics" hreflang="en">Economics</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/physical-sciences-division" hreflang="en">Physical Sciences Division</a></div> </div> <div class="field field--name-field-relatedstories field--type-text-long field--label-hidden field--item"><p>“<a href="../science-medicine/free-thinking" target="_self">Free Thinking</a>” (<em>University of Chicago Magazine</em>, Sept–Oct/14) “<a href="http://news.uchicago.edu/article/2014/03/20/uchicago-expand-online-offerings-partnership-edx" target="_blank">UChicago to Expand Online Offerings in Partnership with edX”</a> (University of Chicago News Office, March 20, 2014) <a href="http://news.uchicago.edu/article/2014/03/20/uchicago-expand-online-offerings-partnership-edx" target="_blank">“</a><a href="http://news.uchicago.edu/article/2013/06/04/uchicago-signs-coursera-begins-online-education-experiment" target="_blank">UChicago Signs with Coursera, Begins Online Education Experiment</a>” (University of Chicago News Office, June 14, 2013) “<a href="http://news.uchicago.edu/article/2011/09/20/book-traces-long-trail-global-warming-scholarship" target="_blank">Book Traces Long Trail of Global Warming Scholarship</a>” (University of Chicago News Office, 11.20.2011)</p> </div> <div class="field field--name-field-relatedlinks field--type-text-long field--label-hidden field--item"><p><a href="https://www.coursera.org/chicago" target="_blank">UChicago Coursera offerings</a>     <img src="http://mag.uchicago.edu/sites/default/files/2015_Summer_Inquiry-cover.jpg" width="140" /></p> <h5>This article originally appeared in the Summer 2015 issue of <em>Inquiry</em>, the biannual publication produced for University of Chicago Physical Sciences Division alumni and friends.</h5> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="../inquiry-archive" target="_self">VIEW ALL <em>INQUIRY</em> STORIES</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://mag.uchicago.edu/sites/default/files/Inquiry_Summer2015.pdf">DOWNLOAD THE LATEST ISSUE (PDF)</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://physical-sciences.uchicago.edu/news/archive" target="_blank">READ ADDITIONAL PSD NEWS</a></div> </div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/climate-change-101-and-beyond" data-a2a-title="Climate change 101—and beyond"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Fclimate-change-101-and-beyond&amp;title=Climate%20change%20101%E2%80%94and%20beyond"></a></span> Tue, 09 Jun 2015 21:53:48 +0000 jmiller 4748 at https://mag.uchicago.edu Chemistry switches https://mag.uchicago.edu/science-medicine/chemistry-switches <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1412_Searcy_Chemistry-switches.png" width="700" height="325" alt="" typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" about="/profile/mrsearcy" typeof="schema:Person" property="schema:name" datatype="">mrsearcy</span></span> <span>Wed, 12/17/2014 - 20:26</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item">“It’s a very sophisticated naturally occurring device. The ribosome basically turns food into babies,” says professor Yamuna Krishnan.     <img src="http://mag.uchicago.edu/sites/default/files/2015_Winter_Inquiry-cover.png" width="140" /><h5>This article originally appeared in the Fall 2014 issue of <em>Inquiry</em>, the biannual publication produced for University of Chicago Physical Sciences Division alumni and friends.</h5> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="../inquiry-archive" target="_self">VIEW ALL <em>INQUIRY</em> STORIES</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://mag.uchicago.edu/sites/default/files/Inquiry_Fall2014_0.pdf">DOWNLOAD THE LATEST ISSUE (PDF)</a></div> <div class="issue-link" style="font-size: 13px; font-weight: normal;"><a href="http://physical-sciences.uchicago.edu/news/archive" target="_blank">READ ADDITIONAL PSD NEWS</a></div></div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/maureen-searcy"> <a href="/author/maureen-searcy"> <div class="field field--name-name field--type-string field--label-hidden field--item">Maureen Searcy</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/inquiry" hreflang="en">Inquiry</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item"><p>Fall/14</p> </div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item">Yamuna Krishnan builds chemical tools with nucleic acids.</div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Professor <a href="https://chemistry.uchicago.edu/faculty/faculty/person/member/yamuna-krishnan.html" target="_blank">Yamuna Krishnan</a> has always loved making things. When she was a child, she and her sister would cook meals, make invisible ink, and grow sugar and salt crystals. They would use whatever they could find in their mother’s kitchen and father’s garden to create something new.</p> <p>Thinking she would carry this passion for building into a career, Krishnan wanted to study architecture. Yet at Women’s Christian College in Chennai, India, she took a chemistry course, where she felt both engaged and adept. She changed fields and now works with chemical architectures, using nucleic acids to build biocompatible synthetic nanoscale machines.</p> <h5>[[{"type":"media","view_mode":"media_original","fid":"2285","attributes":{"alt":"","class":"media-image","height":"111","typeof":"foaf:Image","width":"460"}}]]<br /> A DNA icosahedron (black) held together with aptamers—molecules designed to bind to a specific target—(red) encapsulates molecular cargo (green). A trigger (gray hexagons), folds back the aptamers, opening the icosahedron and releasing the cargo.</h5> <p>Krishnan’s work is influenced by naturally occurring nucleic devices. She cites the ribosome, the cellular machine that arranges amino acids from our diet into all the proteins that make up the human body, using RNA’s template. “It’s a very sophisticated naturally occurring device,” she says. “The ribosome basically turns food into babies.”</p> <p>She enjoys the challenge of complex organizations, where “multitudes of processes perform in concert.” Such complex systems, common in biology’s realm, have become fodder for chemists, notes chemistry chair <a href="http://jordan-group.uchicago.edu/" target="_blank">Richard Jordan</a>. Advances in technology—spectroscopy, microscopy, imaging, and molecular and computational modeling—have allowed chemists to move from studying “relatively simple systems, like conventional organic or inorganic chemicals at a very detailed level,” to complex systems, like the processes that work together to make up a living organism.</p> <h5>[[{"type":"media","view_mode":"media_original","fid":"2286","attributes":{"alt":"","class":"media-image","height":"161","typeof":"foaf:Image","width":"460"}}]]<br /> The I-switch, a DNA pH sensor, functions in a soil-dwelling roundworm’s coelomocytes that serve as scavenger cells for the worm. Image courtesy Yamuna Krishnan.</h5> <p>Krishnan joined the University this summer, one of four biologically inclined chemists hired to help the department both reflect and advance chemistry’s changing landscape. Throughout the past decade, the field has expanded “beyond the classical core areas of organic, inorganic, and physical chemistry into other areas of science where a molecular level of understanding is beneficial,” says Jordan. Those areas include materials science and chemical biology, which both involve complex systems.</p> <p>There’s no clear distinction between chemical biology and the better-known field of biochemistry, Jordan says, but there may be differences in ultimate intention: “Chemical biology describes trying to determine the structures and reactivity of key biomolecules in living systems, how they interact, how they control the processes of life.” Chemical biologists hope to “not only study what’s going on but to manipulate and change it,” relying heavily on chemical synthesis—engineering reactions to create a desired product.</p> <p>One way chemical biologists like Krishnan exploit synthesis is by building molecular tools designed to enter a living cell and perform a particular function. For instance, the ability to measure pH inside an organelle could help to detect and treat diseases. Just as a fever can indicate illness in humans, acidic conditions can indicate illness in cells; lysosomal storage disorders, including Tay-Sachs disease, are associated with acidic conditions in the lysosome. The challenge is getting a tool to work as well in a complex living organism as it does in a petri dish.</p> <p>At her previous institution, India’s National Centre for Biological Sciences in Bangalore, Krishnan developed the first—and as yet only—such device: the I-switch. The DNA-based device “uses a structure called the i-motif, which is at the heart of its switching mechanism,” explains Krishnan.</p> <p>Compared to the complex ribosome, the I-switch is an extremely simple structure that resembles a pair of tongs, closing up under acidic conditions and remaining open under neutral conditions. Attaching molecules called fluorophores, which glow green in the open state, red in the closed state, and yellow and orange in between, Krishnan created a pH meter, a sort of internal litmus test. The switch has thus far worked in worms, and Krishnan hopes eventually to implement it in other living organisms.</p> <p>Also in Bangalore, Krishnan’s lab developed a 3-D nanostructure with a hollow center, called a DNA icosahedron, that helps deliver macromolecules, like drugs or bio-imaging agents, directly where they’re needed. The 20-faced capsule has the most complex solid shape possible to maximize volume and minimize open spaces where the cargo could leak out.</p> <p>To achieve the geometry, she engineered DNA sequences with regions that attract each other; under ideal conditions, the strands fold and connect into an icosahedron. Krishnan designed the structure as a sort of Trojan horse molecule, incorporating a responsive module that opens the capsule in the presence of a chemical trigger, releasing the cargo at its intended target and preventing degradation along the way.</p> <p>At UChicago, Krishnan hopes to apply her synthetic nanomachines to disease models and also develop new devices. While continuing to link her work to detecting and treating disease, she also hopes to focus on fundamental issues of biology on a molecular level, a goal she shares with the department’s other new chemical biologists. She is excited to be back in the classroom. “The best way to connect with and integrate into a new environment is to teach a course,” Krishnan says. “I love teaching chemistry,&nbsp;and I have sorely missed that.”</p> <p align="center"><img src="http://mag.uchicago.edu/sites/default/files/hr.png" /></p> <h2>Roll call</h2> <p>In addition to Krishnan, three other biofocused researchers joined the chemistry department this year.</p> <p><strong><a href="http://dickinsonlab.uchicago.edu/" target="_blank">Bryan Dickinson</a></strong>, assistant professor</p> <ul> <li><em>Research areas:</em> Synthetic chemistry, protein engineering, molecular evolution, and cell biology</li> <li><em>Focus:</em> Developing new technologies to study biological systems, in particular decoding mammalian metabolic regulation, to help understand the mechanisms of and therapeutics for metabolic disease</li> <li><em>Means:</em> Fluorescent probes, protein sensors, and reprogrammed enzymes</li> </ul> <p><strong><a href="https://newfaculty.uchicago.edu/page/raymond-moellering" target="_blank">Raymond Moellering</a></strong>, assistant professor (January 1, 2015)</p> <ul> <li><em>Research areas:</em> Chemical biology, synthetic chemistry, biochemistry, and proteomics</li> <li><em>Focus:</em> Protein modifications and interaction networks in metabolic diseases; synthetically modified protein and peptide therapeutics</li> <li><em>Means:&nbsp;</em>Chemical proteomics, bioorganic synthesis, and cellular and in vivo model systems</li> </ul> <p><strong><a href="http://home.uchicago.edu/~svaikunt/" target="_blank">Suriyanarayanan Vaikuntanathan</a></strong>, assistant professor</p> <ul> <li><em>Research areas:</em> Physical chemistry, soft condensed matter physics, and biophysics</li> <li><em>Focus:</em> Developing and using tools to study complex equilibrium and nonequilibrium systems with the goal of understanding how the organization and information processing of microscopic biological systems behave in a controlled way</li> <li><em>Means:</em> Theoretical and simulation methodologies and statistical mechanics</li> </ul> <p align="center"><img src="http://mag.uchicago.edu/sites/default/files/hr.png" /></p> <p><em>To learn more about chemistry department initiatives, please contact Brian Yocum at 773.702.3751 or <a href="mailto:byocum@uchicago.edu" target="_blank">byocum@uchicago.edu</a>.</em></p> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> <div class="field--item"><a href="/tags/dna" hreflang="en">DNA</a></div> <div class="field--item"><a href="/tags/rna" hreflang="en">RNA</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/physical-sciences-division" hreflang="en">Physical Sciences Division</a></div> </div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/chemistry-switches" data-a2a-title="Chemistry switches"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Fchemistry-switches&amp;title=Chemistry%20switches"></a></span> Thu, 18 Dec 2014 02:26:55 +0000 mrsearcy 4266 at https://mag.uchicago.edu Years of cheers https://mag.uchicago.edu/science-medicine/years-cheers <div class="field field--name-field-letter-box-story-image field--type-image field--label-hidden field--item"> <img src="/sites/default/files/1112_Gibson_Years-of-cheers.jpg" width="1600" height="743" alt="" typeof="foaf:Image" class="img-responsive" /> </div> <span><span lang="" typeof="schema:Person" property="schema:name" datatype="">Anonymous</span></span> <span>Mon, 10/31/2011 - 17:13</span> <div class="field field--name-field-caption field--type-text-long field--label-hidden field--item"><p>(Photo by Jason Smith)</p> </div> <div class="field field--name-field-refauthors field--type-entity-reference field--label-visually_hidden"> <div class="field--label sr-only">Author</div> <div class="field__items"> <div class="field--item"> <div about="/author/lydialyle-gibson"> <a href="/author/lydialyle-gibson"> <div class="field field--name-name field--type-string field--label-hidden field--item">Lydialyle Gibson</div> </a> </div> </div> </div> </div> <div class="field field--name-field-refsource field--type-entity-reference field--label-hidden field--item"><a href="/publication-sources/university-chicago-magazine" hreflang="en">The University of Chicago Magazine</a></div> <div class="field field--name-field-issue field--type-text field--label-hidden field--item">Nov–Dec/11</div> <div class="field field--name-field-subhead field--type-text-long field--label-hidden field--item"><p>For five decades, Stuart Rice and his doctoral students have had great chemistry.</p> </div> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>Crowded onto two high shelves in <a href="http://chemistry.uchicago.edu/faculty/faculty/person/member/stuart-a-rice.html" target="_blank">Stuart Rice</a>’s Gordon Center office, above textbooks on physical chemistry and the kinetic theory of dynamic fluids, sit 107 empty champagne bottles, one for each student whose dissertation Rice has advised in his 54 years at Chicago. Names and dates, some sun bleached, are carefully written across the labels: J. Wenzel, Aug. 19, 1975; Hui Tang, Oct. 28, 1997; Derek Frydel, July 22, 2005. The oldest bottle on the shelf belongs to Robert Harris, SM’59, PhD’60, a chemistry professor emeritus at the University of California, Berkeley, who finished his doctorate in a year and a half. Rice’s most recent graduate is Alice Sheu, SM’03, PhD’08, a pianist who went on to earn a degree from Massachusetts’s Longy School of Music.</p> <p>Rice, the Frank Hixson distinguished service professor emeritus in chemistry, displays the bottles as mementos of the parties that follow final PhD exams. After the corks are popped and the champagne poured—he prefers his dry—he keeps one bottle for himself and gives another to the graduating student. “So there are 107 bottles scattered around the world,” he says. They belong to named professors, physicists at national laboratories, experts in motion perception and heart arrhythmias and geothermal energy. Many are also Rice’s lifelong friends. “Graduate education is very much like creating a new family,” he says. The relationship between mentor and student “is not an abstract exercise in which someone goes through a set of steps following a set of rules. It’s much more intense, much more diverse, much more fluctuating than that.”</p> <p>In the decades since Harris&nbsp; graduated and Rice saved a champagne bottle with his name on it, the collection has become kind of a living chronicle. Each bottle is a story: Michael Lipkin, PhD’84, who became a floor trader on the American Stock Exchange and a bridge-playing expert; Oleh Weres, SB’72, PhD’72, who took the PhD candidacy exam as a College third-year and “came out on top of the whole field.” He received his graduate and undergraduate degrees on the same day, and “bless his heart,” Rice says, “a private ceremony was arranged in the president’s office, to give him his bachelor’s degree before his PhD.”</p> <p>For Rice, the bottles denote achievement, both his students’ and his own. For those working toward their doctorates, they offer “a visual reminder,” he says, “that there has been a history of students here.”</p> </div> <div class="field field--name-field-reftopic field--type-entity-reference field--label-hidden field--item"><a href="/topics/science-medicine" hreflang="en">Science &amp; Medicine</a></div> <div class="field field--name-field-tags field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/tags/chemistry" hreflang="en">Chemistry</a></div> </div> <div class="field field--name-field-refuchicago field--type-entity-reference field--label-hidden field--items"> <div class="field--item"><a href="/physical-sciences-division" hreflang="en">Physical Sciences Division</a></div> </div> <div class="field field--name-field-storymedia field--type-text-long field--label-hidden field--item"><h2 class="media-icon media-icon-slideshow">Slideshow</h2> <object width="200"> <param name="flashvars" value="offsite=true&lang=en-us&page_show_url=%2Fphotos%2Fuchicagomagazine%2Fsets%2F72157628029785826%2Fshow%2F&page_show_back_url=%2Fphotos%2Fuchicagomagazine%2Fsets%2F72157628029785826%2F&set_id=72157628029785826&jump_to="></param> <param name="movie" value="http://www.flickr.com/apps/slideshow/show.swf?v=109615"></param> <param name="allowFullScreen" value="true"></param><embed type="application/x-shockwave-flash" src="http://www.flickr.com/apps/slideshow/show.swf?v=109615" allowFullScreen="true" flashvars="offsite=true&lang=en-us&page_show_url=%2Fphotos%2Fuchicagomagazine%2Fsets%2F72157628029785826%2Fshow%2F&page_show_back_url=%2Fphotos%2Fuchicagomagazine%2Fsets%2F72157628029785826%2F&set_id=72157628029785826&jump_to=" width="200"></embed></object><p><a class="more-link" target="_blank" href="http://www.flickr.com/photos/uchicagomagazine/sets/72157628029785826/">View the images at Flickr</a></p> </div> <span class="a2a_kit a2a_kit_size_32 addtoany_list" data-a2a-url="https://mag.uchicago.edu/science-medicine/years-cheers" data-a2a-title="Years of cheers"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_google_plus"></a><a class="a2a_button_print"></a><a class="a2a_dd addtoany_share_save" href="https://www.addtoany.com/share#url=https%3A%2F%2Fmag.uchicago.edu%2Fscience-medicine%2Fyears-cheers&amp;title=Years%20of%20cheers"></a></span> Mon, 31 Oct 2011 22:13:23 +0000 Anonymous 416 at https://mag.uchicago.edu