Scientific Slug Staff

SCIENTIFIC SLUG STAFF Nicolas Lounsbury, Editor in Chief Computational Mathematics Casey Weiss, Director of Art Physical Anthropology Neuroscience Class of 2013 Class of 2014 Jessica Hodson, Writer & Editor Caitlin Celic, Writer Neuroscience Marine Biology Psychology Chemistry Minor Class of 2014 Class of 2015 Odile Bouchard, Writer & Artist Hanae Armitage, Writer & Editor Biology Biology Environmental Studies Class of 2014 Class of 2016 Titash Chatterjee, Writer Shivam Dave, Writer Biology Computer Science Chemistry Minor Class of 2016 Class of 2015 Quinn Cachola , Artist Alex Infanger, Anthropology Writer Physics Biology Class of 2016 Class of 2015 John Haytko, Cameron Mehrabian Writer , Writer Computer Science Cognitive Science Mathematics Class of 2013 Class of 2016 Nikki Usui, Artist David Shugar, Writer Art Physics Class of 2015 Class of 2014 Jahlela Hasle, Guest Writer & Editor Andrew Kornfeld, Writer & Artist Cognitive Science Psychology UC Berkeley Class of 2013 Neuroscience Class of 2013 Art by Odile Bouchard Interested in Science Journalism? Robert Irion, director of UCSC’s Science Communication Program, offers an under- graduate course each spring quarter: SCIC 160 / BIOE 188, Introduction to Science Writing. Students learn about news and feature writing for public audiences, culminat- ing in a magazine-length story about campus research. For details, contact the SciCom Program at [email protected] or x9-4475. Life, which we once believed to be exceptional, may very well be inevitable. » p.23 » p.17 » p.10 » p.7 » p. 14 CONTENTS Scientific Slug 6 Seeing Green: Fluorescent Detection of Poisonous Urushiol By Jessica Hodson 8 The Rhythm Schism: Who’s got rhythm? By Caitlin Celic » p.23 10 Telomere Structures Unfold to Reveal Possible Anti-Cancer Therapy By Hanae Armitage 12 From Polar bears to Brown Bears: Genomic Footprints Reveal Patterns of Evolution By Titash Chatterjee 14 Can You Grasp This Concept? By Cameron Mehrabian 16 Solar Greenhouse: Two Birds » p.8 With One Stone By David Shugar 19 A New Perspective on Sight and Technology By Shivam Dave 20 The Golden Age By John Haytko 22 Living Systems Happen By Andrew Kornfeld & Jahlela Hasle » p.13 6 BIOCHEMISTRY Seeing Green: Fluorescent Detection of Poisonous Urushiol By Jessica Hodson Do you know how to spot bilayer and, after a series of enzymatic shiol. In her lab at UC Santa Cruz, Dr. poison oak? If it’s shiny, watch your breakdowns, attaches itself to proteins Braslau explores the practical applica- hiney, leaves of three, let it be. Not in the membrane. tions of radicals. bad. I’ll give you partial credit for that “This [altered protein] is the Radicals are reactive molecules answer -- it did once represent the cut- thing that your immune system sees with an odd number of electrons: they ting edge in poison oak detection. If and goes Intruder! Mount the defenses!” lack the partner electron they need you want full points though, talk to Dr. Braslau explains. to make a bond. In order to find their Rebecca Braslau. She can see traces missing piece, radicals attack the bonds of that shiny, dangerous oil in poison in other molecules and steal their elec- oak, called Urushiol, hours later and Urushiol is trons. This prompts a vicious cycle that miles away from any plant on the heel dangerous resembles the plot of virtually any epi- of your shoe. That’s right, Dr. Braslau because that sode of Game of Thrones. and her colleagues at UC Santa Cruz greasy carbon chain In the beginning, all is fine and have discovered a way to make Uru- looks a lot like the fats dandy (more or less) between the main shiol residue glow in UV light. families; they have stable bonds. Then Dr. Braslau’s work is classic in our cell membranes. one day someone’s head gets chopped -- she found a problem, she solved it. off. When a radical attacks a bond and The poison oak scattered all over the steals an electron, it creates another California wilderness threatens many radical. In Game of Thrones, when you of us: 50-70% of the adult American Whilst brazenly defending chop off someone’s head, their family population is allergic. Although most our honor, our immune system dam- gets a little upset and swears to avenge of us know to avoid the plants, we still ages our skin cells, provoking that their death. Unfortunately, revenge end up with it on our clothes, oblivi- itchy, oozy, crimson rash that we all doesn’t do much in the way of repair- ous to the oil lurking in the folds. It’s know and dread. ing bonds - quite the contrary - it creates not until the later onset of itchy skin For Dr. Braslau, the threat of more enemies. The same holds true for that we suspect up close and personal poison oak is especially acute. While radicals; they simply perpetuate the de- contact with Urushiol. she is extremely allergic, her geolo- struction. Urushiol in poison oak is part gist husband is not. He would go out As you might expect, due to of a family of compounds known as to survey land, come home, and unin- their reactive and destructive nature, Catechols. Catechols have a six carbon tentionally give her poison oak. One radicals harm living things. However, ring with two alcohol groups and, as time, she recalls, “He got it on his arm if directed carefully, their power can be Dr. Braslau puts it, “a long greasy car- and he slept with his arm around my harnessed for good. Dr. Braslau works bon chain.” Urushiol is dangerous be- torso...I got it from my neck all the way with nitroxides, carbon compounds cause that greasy carbon chain looks a down to my underwear, just all over with an unpaired electron spread over lot like the fats in our cell membranes. the front of me. It was horrible and a nitrogen atom and oxygen atom. When we get the oil on our skin, it he felt so bad, he had no idea he had Around the time of her particularly bad sneaks right through the membrane it there.” After spending three weeks run-in with Urushiol, Dr. Braslau had in agony with contact dermatitis (and been exploring some specific nitroxide this was not the first time), Dr. Braslau interactions. Two of them became the thought to herself, “I should be able to foundation for her fluorescent Urushiol do something about this.” discovery. As it turns out, her work with In one project she studied the radical chemistry put her in a unique interplay between nitroxides and fluo- position to solve her poison oak prob- rescent dye. When she bonded a nitrox- lem by creating a way to detect Uru- ide to a fluorescent dye, the unpaired radical electron quenched the dye’s Scientific Slug | February, 2014 7 fluorescence. The resulting compound ing the two react! could have other biomedical uses: is called a pro-fluorescent nitroxide, Dr. Braslau’s pro-fluorescent Urushiol is related to catecholamine meaning that the fluorescence is cur- nitroxide plus boron mixture is like neurotransmitters in the brain such rently off but can be switched back vinegar, Urushiol is like baking soda. as epinephrine, norepinephrine and on when there is no longer a radical When this mixture comes into contact dopamine. This might mean that Dr. quenching the fluorescence. with Urushiol, it glows, so any ob- Braslau’s method could detect these In a separate project, Dr. server can locate the Urushiol with UV compounds. Effective identification of Braslau attempted to utilize com- light. As soon as she could, Dr. Braslau dopamine distribution, for example, pounds containing the element boron went out into the woods, dripped her could be instrumental in Alzheimer’s to generate radicals on carbon atoms, solution on some poison oak, pressed research. but was unsuccessful. Ideally, she it onto a paper towel, and held up a Although the Urushiol spray could create a carbon radical using a UV light. This is what she saw: project is moving at a relatively slow boron compound and a nitroxide. Dr. Braslau struggled to achieve this until she saw the research of Swiss col- league, Philippe Renaud. He reacted nitroxides with boron attached to a catechol, like Urushiol, and success- fully generated carbon radicals. Suddenly she had her big, as she describes it, Eureka! moment -- she could use a Urushiol-boron compound to generate carbon radicals with nitroxides! These carbon radicals could then pair up with the nitroxide radi- Left: Classic Poison Oak with “leaves of three” cals to restore the quenched fluores- Right: Fluorescence from Urushiol left behind by Poison Oak seen in UV light cence. She went back into the lab to try it and “it worked...the first time, it was really exciting” she says. Her profound discovery not pace, Dr. Braslau has another practi- Catechols like Urushiol aid only illuminates a dangerous oil oth- cal applications project underway. She the generation of a carbon radical be- erwise invisible to the human eye, but hopes to develop an alternative to the cause their structure, due to the six- also lays down the foundation for the dangerous plasticizers found in PVC carbon benzene ring, easily carries the development of a spray anyone could pipes, electric cables, clothing, and extra electron that the nitroxide do- use at home or in the field. This is pos- medical fluid bags. nates. This stabilization makes it possible because the reaction can be made The practicality of Dr. Braslau’s sible for the nitroxide to bond with the to occur in a safe solvent: acetone (nail work makes it wonderful. She took her Urushiol-boron compound and kick- polish remover) at room temperature profound scientific knowledge and ap- out a carbon radical.

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