Spring 2012 Issue by Carolina Scientific

Carolina Scientific

Carolina

sc覺ent覺fic Undergraduate Research Magazine Spring 2012 | Volume 4 | Issue 2

a breakthrough for HIV-AIDS treatment page 23

Carolina

sc覺entific Mission Statement: Founded in Spring 2008, Carolina Scientific serves to educate undergraduates by focusing on the exciting innovations in science and current research that are taking place at UNC-Chapel Hill. Carolina Scientific strives to provide a way for students to discover and express their knowledge of new scientific advances, to encourage students to explore and report on the latest scientific research at UNCChapel Hill, and to educate and inform readers while promoting interest in science and research. From the Editor: As Carolina Scientific grows, we hope that our publication continues to foster strong relationships among the creative scientific thinkers at UNCChapel Hill. While researchers work to understand the stories of science, we strive to bring their discoveries to life. This issue, we are excited to provide our readers with an interesting and informative collection of the innovative research occurring in our community. Enjoy! - Garrick Talmage

on the cover

Executive Board Editor-in-Chief Applied Sciences Life Sciences Physical Sciences Design Design Copy Fundraising

Garrick Talmage Keith Funkhouser Kelly Speare Dasha Gakh Kati Moore Hema Chagarlamudi Sophie Liu Kandace Thomas

Contributors Writers Sarayu Kumar Olivia Wayne Morgan Locklear Amanda Raymond Casey Clements Hannah Aichelman Sneha Rao Matt Leming Trent Teague Yurhee Lee Kelsey Ellis Hetali Lodaya Dylan Campfield Bhavesh Patel Wylder Fondaw Olivia Snyder Shamra Byrne Designers Madelyn Roycroft Alexis Balinski Calvary Diggs Paige Derouin Olivia Wayne Paige Tummons Shalija Amin Copy staff Lauren Walls Olivia Snyder Jackson Trotman Amelia Lorenzo Calvary Diggs Sean Xing Matt Leming

Electron microscope capture of HIV cells, seen as dots on a white blood cell. Image from the CDC/C. Goldsmith, P. Feorino, E. L. Palmer, and W. R. McManus. See page 23 for the full story.

carolina_scientific@unc.edu carolinascientific.web.unc.edu facebook.com/CarolinaScientific @uncsci

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contents 14

features 20

Matt Leming

We Are Small But Mighty Microbial Life at the Bottom of the Sea Follow Dr. Andreas Teske as he travels to one of Earthâ&#x20AC;&#x2122;s most inhospitable environments.

Kelsey Ellis

Computerized Organs: Medical Imaging Analysis at UNC

Treatment as Prevention

X-Raying the Skeleton of the Cell

Food for Thought: The Effect of Maternal Diet on Brain Development of Offspring

A Breakthrough for HIV-AIDS

Trent Teague

Yurhee Lee

Dr. Myron Cohen explores the use of antiretroviral drugs to stop AIDS before it starts.

Hetali Lodaya

briefs

Growing Pains

A Dynamo in the Brain

Dylan Campfield Bhavesh Patel

Pain, Pain, Go Away

Scrunch Time

Groin in the Right Direction

Tiny Motors

Humanized Mice Accurately Mirror the Human Immune Response to HIV Infection

Sarayu Kumar

Olivia Wayne

Morgan Locklear

Words in the Mouth of the Speechless

She Thinks My Croak is Sexy

Olivia Snyder

articles

Amanda Raymond

Spinal Muscular Atrophy: The Search for a Cure

Shamra Byrne

Casey Clements

Navigating the Maze of Organic Synthesis

Hannah Aichelman

Wylder Fondaw

Fibrin: The Elastic Bands of the Human Body

Sneha Rao

interview Catching up with Alexandru Bacanu Garrick Talmage

seniors Life After Graduation

Pain, Pain, Go Away Sarayu Kumar

f two people are in a car accident and both happen to walk away relatively injury-free from the site, it is extremely puzzling that one may experience chronic pain for decades while the other may have only acute pain that goes away in a week or two. Research led by Dr. Samuel McLean of the UNC School of Medicine’s department of anesthesiology will explore why these differences in outcomes occur. Dr. McLean and his interdisciplinary team recently received a five-year, $3.5 million grant from the National Institutes of Health to examine the process of chronic pain development after car accidents. Dr. McLean’s study will also examine the development of post-traumatic stress disorder (PTSD), a type of anxiety disorder that can occur in some people after a traumatic event involving the threat of injury or death.1 The study will focus on African-Americans because

Scrunch Time Olivia Wayne

ost people have no idea how many coordinated events an embryo must orchestrate in order to change its shape. Dr. Stephen Rogers of UNC-Chapel Hill’s biology department has been investigating this very process to study

Figure 1. Dr. McLean hopes that the results of this study help will result in improved treatments for individuals involved in car accidents.

evidence suggests that AfricanAmericans may be at increased risk for chronic pain development and PTSD.2 Even after adjusting for socioeconomic disadvantage African-Americans have been found to experience a higher burden of pain in both clinical and experimental settings.2 Dr. McLean’s team will be assessing discrimination as a potential cause for chronic pain because discrimination remains a social reality in the United States that may worsen health outcomes in a number of ways. The study will also examine genetic, physiological and psychological factors that may contribute to vulnerability to chronic pain development. The adrenergic nervous system, which is responsible for the body’s “fight-or-flight” response,

will be carefully observed because it is noted to influence persistent pain.3 This study will involve approximately 1000 African-Americans. In addition, since Dr. McLean has already collected data on 1000 European-Americans, his team will be able to assess ethnic differences in chronic pain development. Dr. McLean hopes that the results of this study help will result in improved treatments for individuals involved in car accidents.

individual cell contractility. During an early stage of embryonic development called gastrulation, the embryo folds in on itself to form an external furrow and three tissue layers. Dr. Rogers elected to use cell lines from Drosophila melanogaster, a common species of fruit fly because of their highly manipulatable genes, a necessary characteristic for his research.1 Genetics were

used to isolate and identify the steps in this folding process. According to Dr. Rogers, “Some of the cells that originate on the belly or the ventral surface of this fly are going to give rise to the mesoderm, and in order for them to do that, they have to go from this outside layer to the interior of the embryo.”2, 3 The individual tissue cells begin this process by acti-

References

1. PubMed Health. Post-traumatic stress disorder. http://www.ncbi.nlm. nih.gov/pubmedhealth/PMH0001923/ (accessed Feb 17, 2012). 2. Interview with Samuel McLean, M.D., M.P.H. 2/17/2012. 3. McLean, S. Spine 2011, 36, S226S232.

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Figure 1. Before and after the Fog activation. Top: The cells visibly pucker. Bottom: Fluorescence microscopy shows activated actin filaments in green. Image courtesy of Dr. Stephen Rogers.

vating myosin, a motor protein, in their apical, or outer, domain. The myosin squeezes the actin cytoskeleton, changing the cuboidal shape of the cells until

Tiny Motors Morgan Locklear

r. Richard Cheney of UNCChapel Hill’s department of cell and molecular physiology has always been intrigued by how things move within a cell. Cellular movement is especially important to the special sense of hearing. Motor proteins have the ability to stretch open a channel within the inner ear, which can allow humans to hear. Dr. Cheney is intrigued by a class of myosin motor proteins that aid in the movement of certain components within the cell.1 Myosin is a motor protein that moves along actin filaments through the use of ATP and serves several important functions for cellular processes. Cheney has set out to find the functions of these motor proteins, specifically for a class of myosin known as myosin-X.

they are shaped like a wedge. This change in conformation is what causes a portion of the embryo to curve in on itself.2 Dr. Rogers’s research focuses on the signaling pathways that trigger the contractile response in individual cells. These pathways may be compared to a switch that, when functioning properly, turns on and off.2 However, when the signal can no longer be regulated, the cell behaves abnormally. In some cases, it resembles a metastasized tumor cell. Thus, it is the research team’s hope that their work on epithelial tissue will deepen the scientific community’s understanding on diseases such as As demonstrated in Figure 1, a striking discovery is that myosin-X is found to localize itself on the tips of the filopodia of cells. Filopodia are actin-based extensions that aid in the locomotion of the cell but are also “thought to function as cellular sensors in processes such as nerve growth and blood vessel development.”2 Dr. Cheney is attempting to discover the purpose of myosin-X’s localizing itself at such a particular area. Dr. Cheney proposed the idea of myosin-X being used with cargo, elements transported in a cell. The type of cargo being transported and its purpose remain unknown. All of these research questions seek to understand how myosin-X relates to human physiology and its cellular processes. Dr. Cheney hopes that his research can be used to understand the causes of deafness and to help with treatments for it.

cancer and hypertension. In preparation for their conformational change, the cell secretes a protein called folded gastrulation, or Fog (Figure 1). Last year, the research team became the first to successfully identify the gene for the Fog receptor.2 This new information will give the team a more complete picture of the initial steps for cell contractility. References

1. Rogers, S. L.; Rogers, G. C. Nat. Protoc. 2008, 3, 606-611. 2. Interview with Stephen L. Rogers, Ph.D. 2/8/2012. 3. Email with Stephen L. Rogers, Ph.D. 2/25/2012.

Figure 1. CAD Cells transfected with GFP-Myo10 (green) and stained for actin filaments (red). Images courtesy of Drs. Taofei Yin and Richard Cheney.

References

1. Interview with Richard Cheney, Ph.D. 2/3/2012. 2. Kerber, M.; Jacobs, D.; Campagonla, B.; Dunn, T.; Yin, T.; Sousa, A.; Quintero, O.; Cheney, R. Curr Biol. 2009, 19, 967.

WORDS

in the Mouth of the Speechless Amanda Raymond, Staff Writer

ith today’s modern technology, many would agree that the value of speech has declined. Text messaging and instant messaging have decreased the desire to communicate verbally. Many of us take the ability to speak for granted and do not even realize that some are unable to do so. Professor Benjamin D. Philpot, Ph.D., investigates individuals stricken with a disorder called Angelman syndrome, for which one of the main symptoms is the loss of speech.1 Because of the intensive research done by Dr. Philpot and researchers at UNC-Chapel Hill, physicians are one step closer to giving individuals with this disorder another chance at speech and a better life. Angelman syndrome is a genetic neurological disorder with no effective therapy. It affects one out of every fifteen thousand people.2 The disorder is characterized by loss of speech, epilepsy, intellectual disability, hyperactivity, sleep disorders, movement and balance disFigure 1. Children with Angelman orders and develsyndrome usually have a “happy and excitable demeanor.” Image opmental delays.3 courtesy of Dr. Benjamin Philpot. Infants with An-

gelman syndrome appear normal at birth, but noticeable signs of this disorder occur by six to twelve months of age, when individuals begin to miss developmental milestones such as sitting up and walking.1 Children with this disorder usually have a “happy and excitable demeanor Dr. Benjamin Philpot along with frequent smiling, laughter and hand-flapping movements” (Figure 1).3 With age, the excitability lessens, and sleeping disorders can improve.3 Though these patients are expected to have normal life spans, they will continue to have intellectual disabilities, severe speech impairments and seizures throughout their lives.3 “The broad focus of our research is trying to understand how the brain anatomy, function and plasticity is disrupted in the brain of individuals with Angelman syndrome,” Dr. Philpot explained.2 As one of the key researchers of this disorder at UNC, he strives to determine if there is a way to fix or reverse this problem. “It was not until ten years into my neuroscience research that I learned of Angelman syndrome for the first time,” Dr. Philpot confessed while describing how the disorder is fairly uncom-

Carolina Scientific mon.2 He says that it was a collaboration with a friend at Duke University, Dr. Mike Ehlers, that encouraged him to undergo his research.2 Meeting individuals with the syndrome put even more gas on the fire for Dr. Philpot. “It really put a face on the disorder,” he said, “to meet individuals with Angelman syndrome and their families” (Figure 2).2 According to an article written by Dr. Philpot and the group of UNC researchers in the scientific journal Nature, Angelman syndrome is “caused by deletion or mutation of the maternal allele of the ubiquitin protein ligase.”4 Like most genes, both the maternal and paternal alleles of this Ube3a gene are inherited, but unlike most genes, the paternal allele is silenced in brain cells; therefore, the maternal allele is the only one that can be expressed. When this allele is deleted or mutated, the necessary Ube3a proteins are not produced, resulting in Angelman syndrome. Only in the brain cells is the paternal allele silenced; in other body cells, both Ube3a gene alleles are expressed. This led Dr. Philpot and the group of researchers to believe that there could be some way to activate the paternal allele because although it was silenced, it was perfectly intact. 4 Awakening the paternal allele would mean the possibility of treating the disorder. After over three years of research and experimentation, Dr. Philpot and his colleagues discovered “twelve topoisomerase I inhibitors and four topoisomerase II inhibitors that unsilence the paternal Ube3a allele.”4 In other words, the researchers learned that certain drugs can activate the silenced paternal allele. The article also demonstrates that the drugs can have long-lasting effects when administered to mice that had Figure 2. Individual with Angel- been genetically altered to model Anman syndrome. Image courtesy of Dr. Benjamin Philpot. gelman syndrome.

This enduring effect could “indicate that a single course of drug treatment has the capacity to permanently modify expression of Ube3a” (Figure 3).4 The researchers not only discovered a way to get the paternal allele working Figure 3. The brain on the bottom again but also is the mouse’s brain with Angelman syndrome. The brain on the top shows that the drugs the increased brain activity of the same have enduring mouse’s brain with Angelman syndrome effects. after the treatment was administered. Dr. Phil- Image courtesy of Dr. Benjamin Philpot. pot affirms that he is working hard to advance these drugs towards clinical trials, but they are not quite ready to take that step. It is difficult to predict when these drugs can be tested in human clinical trials since factors like the correct dosage, delivery schedule and effectiveness of the drug for humans are still unknown. Although great strides have been taken, research and experimentation still continue while Dr. Philpot and the team of researchers at UNC strive towards a cure for Angelman syndrome.2 To learn more about research to find a cure for Angleman Syndrome and how you can help, visit the Angleman Syndrome Foundation at www.angelman.org. References

1. NINDS Angelman Syndrome Information Page. http:// www.ninds.nih.gov/disorders/angelman/angelman.htm (accessed Feb 3, 2012). 2. Interview with Benjamin D. Philpot, Ph.D. 1/26/2012. 3. Angelman Syndrome. http://ghr.nlm.nih.gov/condition/ angelman-syndrome (accessed Feb 3, 2012). 4. Huang, H-S.; Allen, J. A.; Mabb, A. M.; King, I. F.; Miriyala, J.; Taylor-Blake, B.; Sciaky, N.; Dutton, J. W.; Lee, H-M.; Chen, X. et al. Nature 2011, 481, 185-191.

She Thinks My Croak is Sexy:

The Complexity of Mate Choice in Female Plains Spadefoot Toads Casey Clements, Staff Writer

emale mate choice is often overlooked as a simple process — girl picks boy, right? Wrong — as the study of sexual communication in biology grows, innovative research projects are delving into the complex neurobiological, endocrinological and physiological processes that determine and influence this seemingly artless selection as well as into the evolutionary processes and pressures that have promoted the development of these behaviors. Although the role of communication in mate selection appears in many different animal species, countless frog and toad species, including túngara and South African clawed frogs, have become well known in the animal behavior community for their elaborate selection processes. Current research conducted by the Burmeister laboratory at UNC-Chapel Hill, led by Dr. Sabrina Burmeister, is at the forefront of behavioral endocrinology, or behavior influenced by hormones produced by the body. Their research focuses on the plains spadefoot toad (Spea bombifrons), a species commonly found in arid desert areas of the southwestern United States (Figure 1). This species approaches mate selection the same way as most frog and toad species do; females choose the most attractive male based on his croak or call via phonotaxis, or movement towards Figure 1. A plains spadefoot toad in its natural habitat on Dr. Pfennig’s a particular field site in Arizona. Image courtesy of sound (Figure Dr. Karin Pfennig. 2). However, the females also exhibit a perplexing behavior dependent almost entirely on body condition. Accord-

ing to Dr. Burmeister, “Females who are in good body condition [i.e., those that have a lot of fat] prefer conspecific mating [mating within the species]; those who don’t often prefer to mate with a different species.”1 As a result, unhealthy females will Dr. Sabrina Burmeister choose the distinctly different mating call of a separate species, the New Mexico spadefoot toad (Spea multiplicata), whose range overlaps that of the plains spadefoot toad. For those familiar with theories on speciation, evolution and sexual behavior in animals, this behavior is quite an unusual occurrence in nature. Dr. Karin Pfennig, another UNC-Chapel Hill professor involved in spadefoot toad research, has discovered that such behavior in female plains spadefoot toads is no mistake. As desertdwelling animals, female spadefoot toads hatch tadpoles that are faced with a short window of time to grow and develop before the small pool that they call home evaporates into the desert air. Females with poor body condition, or low fat content, have evolved to realize the predicament of their offspring and are therefore more inclined to mate with the New Mexico spadefoot toad (S. multiplicata), a species with a faster growth rate during the metamorphosis of the tadpole, thereby securing the survival of a greater number of the female’s offspring and increasing her fitness. Dr. Burmeister is interested in how hormonal mechanisms control the mating preferences of female spadefoot toads. Nick Garcia, a graduate student in the Burmeister laboratory, looked into the effects of a hormone called leptin on these toads. Leptin, the protein product of the obese (ob) gene, is a fat-secreted hormone that is integral to food intake regulation and influences almost

Carolina Scientific every physiological system in juvenile and adult mammals.2 Dr. Burmeister further clarified that “leptin functions to signal to the individual what their energy budgets should be.”1 Disruptions in leptin signaling, which has primarily been studied in mammals, have been connected to increased obesity. However, in frogs and toads, leptin is expressed in both body fat and other tissues, and its effects are not as clearly understood or studied. Previous studies on the effects of leptin on amphibians have demonstrated that the Figure 2. A male plains spadefoot hormone influtoad mid-croak. Image courtesy of ences limb deDr. Karin Pfennig. velopment in the metamorphosis of South African clawed frog tadpoles, but little research has been conducted on its effects on sexual behavior in amphibians.2 Dr. Burmeister’s original hypothesis was that the addition of leptin to female spadefoot toads in poor body condition would cause the female to start choosing the calls of males within her species because the hormone would give the body a sense of higher fat content. To conduct the experiment, the females are divided into three categories: a control group injected with a saline solution, an antagonist group with opposed leptin receptors and an experimental group with leptin added. Each female is then placed individually in a circular arena with two speakers on opposite sides, one speaker playing the call of a male S. bombifrons and the other playing the call of S. multiplicata. After approximately 30 minutes, researchers would record the speaker, right or left, that was first touched by the female. The results came as quite a surprise to the researchers — they found that approximately 70 percent of leptin-injected female toads actually went towards the speaker playing the S. multiplicata call. These results contradict Dr. Burmeister’s original hypothesis and therefore present a unique and novel challenge to the researchers as they

must now formulate and design new hypotheses and experiments, respectively, to explain these results and the physiological processes responsible. Dr. Burmeister believes the manipulation of leptin in these toads is “physiologically relevant” and that the effects of leptin in toads may turn out to be “more complex than in mammals because in mammals, it is produced primarily by fat tissues and has primarily one function,”1 whereas in toads, the hormone addition may cause a multitude of changes. The Burmeister laboratory is currently focusing on the continuation of these leptin experiments as well as follow-up experiments as measuring the natural levels of leptin with the use of anti-leptin antibodies. Dr. Burmeister understands these behaviors to be a result of evolutionary change in the nervous system, a topic in which she has shown interest since her undergraduate years. These research developments, although made with the seemingly obscure spadefoot toad, are extremely important to our understanding the effects of hormones on behavior, especially across different animal systems as leptin research is currently being conducted on many mammal species as well. The Burmeister laboratory and its recent results are an excellent representation of how fortuitous science can be, making it the exciting and unpredictable field that it is today.

Figure 3. A rudimentary outline of the physiological processes involved in mate selection in many amphibian species. Image courtesy of Dr. Sabrina Burmeister.

References 1. Interview with Sabrina Burmeister, Ph.D. 1/31/2012. 2. Crespi, E. J.; Denver, R. J. Proc. Natl Acad. Sci. USA 2006, 103, 10092-10097.

Navigating the Maze of Organic Synthesis Hannah Aichelman, Staff Writer

hen most students at UNC-Chapel Hill hear the words “organic chemistry,” their immediate reaction is to turn around and walk the other way. Walking through Caudill Laboratories on the way to Dr. Jeffrey Johnson’s office, it is not difficult to understand this reaction. The posters on the wall have titles beyond comprehension, and the labs are filled with students in white coats surrounded by equipment that looks too complicated to ever understand. But for students working in Dr. Johnson’s laboratory, this is all part of a day’s work. Dr. Johnson and his students are looking to prove that organic chemistry is a fascinating and incredibly important field. Dr. Johnson’s laboratory consists of ten graduate students and one postdoctoral student who focus on the topics of organic synthesis and chemical reactivity. These students are studying how chemical reactions work, what

Figure 1. A diagram of a molecule of zaragozic acid C, which was synthesized in Dr. Johnson’s laboratory. Image courtesy of Dr. Jeffrey Johnson.

steps molecules go through to get to a final desired product, and how to make reactions and molecules that no one has seen before. Dr. Johnson describes the process as having a molecule navigate a maze, except the Dr. Jeffrey Johnson scientist has to help it along the correct path in order for it to reach the desired end product.1 Organic chemists have the ability to synthesize their own — and possibly even better — versions of molecules found in nature by developing reactions to create them. This task is accomplished by a method known as retrosynthesis, which is an exercise in working backward from the desired molecule to something that can be bought in bulk and easily handled in a laboratory.1 In order to successfully complete a retrosynthetic analysis, an encyclopedic knowledge of chemical reactions is needed. The walls of Dr. Johnson’s office are filled with books describing unique chemical reactions, any one of which could take the molecule in question to where it needs to be. The process begins when a new reaction must be developed. Dr. Johnson’s laboratory has had many successes with designing reactions to create brand new products. One example is zaragozic acid C (Figure 1), which has the potential to lower cholesterol and to serve as

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Three of Dr. Johnson’s graduate students, Ryan Carris, Justin Malinowski and Michael Corbett, hard at work in the lab.

Figure 2. A molecule of pactamycin, which students in Dr. Johnson’s laboratory are working on synthesizing. Image courtesy of Dr. Jeffrey Johsnson.

a chemotherapy medication. While the drug is works on creating new reactions, the students effective in both aspects, it causes negative side often create innovative structures, some of effects and is too toxic to use.2 Pactamycin is which have potential medicinal functions as seen another molecule that the laboratory is working with zaragozic acid C and pactamycin. When the on synthesizing (Figure 2). It has the potential to structures have an interesting characteristic, such be an antitumor, antimalarial and antimicrobial as a functional group in an uncommon place, medication but is also too toxic to be administered the molecule is sent to another laboratory that to patients. conducts tests on its possible significance.1 While Making new molecules is a complicated some of the novel structures could have medicinal process as demonstrated by a graduate student purposes, multiple structures still remain without in Dr. Johnson’s laboratory who a purpose or function. has been working on the single Organic chemistry is a In this line of work, the step of adding two nitrogen unique field. In this line of work, atoms to a molecule for two idea ‘I have no idea how the idea “I have no idea how to years. Once the scientist has to make that’ is actually make that” is actually exciting. worked backwards from the Because of the incredible exciting. complicated molecule to a complexity of the field, scientists small starting material, the often encounter failure. With work in the forward direction begins. This part of new reactions working only about five percent of the process involves taking the starting material the time, the successes are even sweeter. “One of and slowly adding on to it the different molecules the things I really like about my job,” Dr. Johnson determined in the retrosynthetic analysis until the states, “is the creation of new knowledge, new desired end product is reached.1 compounds, things no one has ever made before. When most people think about organic That is what makes organic synthesis unique.”1 synthesis, they probably think about making new pharmaceuticals. Currently, Dr. Johnson’s laboratory does not synthesize molecules for References medicinal use; however, because medicinal 1. Interview with Jeffrey Johnson, Ph.D. 2/3/2012. chemistry is a growing field, Dr. Johnson hopes to 2. Nicewicz, D. A.; Satterfield, A. D.; Schmitt, D. C.; Johnmove in that direction in the future. Because the lab son, J. S. J. Am. Chem. Soc. 2008, 130, 17281-17283.

Fibrin: the Elastic Bands of the Human Body Sneha Rao, Staff Writer

ccording to the Centers for Disease Control and Prevention (CDC), there are more than 2 million heart attacks and strokes a year. Of these 2 million, 800,000 result in death. Due to such staggering statistics, heart disease has slowly made its way to the top of the CDC’s list of leading causes of death.1 The recent increase in cardiovascular disease has set researchers on a race to discover as much as they can about the heart. UNC-Chapel Hill’s Computer Integrated Systems for Microscopy and Manipulation (CISMM) has joined in on the cause and has honed in on one of the most important parts of the cardiovascular system: blood clots. Dr. Michael Falvo, research professor in the department of physics and astronomy, and Drs. Oleg Gorkun and Susan Lord of the department of pathology and laboratory medicine are working on understanding the mechanical properties of fibrin, a protein that forms the structural framework of blood clots. Before the formation of a blood clot, fibrinogen molecules travel through the blood stream. Any damage to the blood vessel wall sets off a biochemical process that converts the free-floating fibrinogen into fibrin. The fibrin molecules then string together to form a network, somewhat like a cobweb, and other components of a blood clot such as platelets and red bloods cells get caught in the network of fibrin (Figure 1). Although blood clots are Figure 1. Fibrin fibers form a dense essential in renetwork made up of red blood cells pairing damage and platelets. Image courtesy of Dr. in the blood Michael Falvo.

vessels, they can also be very dangerous if they break away and block part of a blood vessel. A blood clot that blocks a blood vessel or artery is known as an embolism. Although embolisms are most commonly found in the legs and feet, arDr. Michael Falvo terial embolisms in the heart or the brain can cause heart attacks and strokes, which can be fatal. “Recent statistics on heart attack patients indicate that there is a correlation between heart attack patients and stiff clots,” said Dr. Falvo. “Folks that have heart attacks seem to have stiffer blood clots.” Dr. Falvo believes that since the fibrin molecules comprise most of the structural framework of the blood clot, knowing more about fibrin’s mechanical properties may explain the correlation.2 Since the fibrin protein is so integral to forming the structure of the blood clot, learning more about an individual fibrin molecule’s mechanical properties is crucial. This is where the physics of biology becomes important. Dr. Falvo’s laboratory is mainly interested in the elastic properties of the fibrin protein. To study the extent of fibrin’s elasticity, individual fibers were studied on the microscopic level using an atomic force microscope. By isolating individual fibers and using a very fine tip to stretch the fiber and letting it bounce back, Dr. Falvo and his collaborators were able to measure forces tolerated by the fibrin in the horizontal and vertical directions.1 This gave them a sense of how elastic the fibers can be. “We found that fibrin fibers act like rubber,” said Dr. Falvo. “They stretch three to four times their original length, but their structure is nothing like rubber. It’s a mystery as to how it can act like rubber even though it does not share a similar structure.”2 Fibrin has a crystal-like structure but rubber-like qualities.

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Figure 2. The fibrin molecule is made up of two sets of three amino acid chains that are helically coiled in the middle. The ends of the protein are made up of amino acid clusters. Amino acid chains extend from the helically coiled regions and connect to other fibrin proteins. Image courtesy of Dr. Michael Falvo.

The key now is to find what part of the fibrin protein enables it to have such elastic properties. Dr. Falvo’s laboratory is currently trying to determine exactly which part of the molecule allows it to behave like an elastic band. The fibrin protein is a very large protein that is made up of two sets of three amino acid chains that twist and coil into a fiber. The middle region of the protein is made up of helical amino acid chains called α-helix coils. The helical chains also contain protruding amino acid chains called αC connectors (Figure 2). The ends of the fibrin protein have two clusters of proteins called γ-nodules and β-nodules (Figure 2).3 Researchers at other universities are also examining the origins of the fiber’s elastic property and believe that the twisted helical regions of the fiber are responsible for the fiber’s elasticity. Dr. Falvo’s laboratory has recently found experimental evidence that may contradict this understanding of fibrin. The laboratory isolated individual fibers, stretched them and then measured the amount Figure 3. Stretching an individual fibrin fiber using an Atomic Force Microscope to determine mechanical properties. Image courtesy of Dr. Michael Falvo.

of time that they took to recoil back (Figure 3).2 “The fibers snap back extremely fast, in a few hundred microseconds,” said Dr. Falvo.2 “The time that it takes to snap back puts constraints on what part of the protein could be responsible for the stretchiness.”2 Dr. Falvo’s laboratory hypothesizes that the αC region that extend from the α-helix coils and connect to other fibrin proteins are responsible for fibrin’s elasticity (Figure 2).4 Future research may potentially link the quaternary structure of the αC region to the proteins’ primary amino acid sequence. Along with determining a possible genetic basis for the protein structure, researchers could study the same region of fibrin in heart attack patients who seem to have stiffer clots. “By some measures, blood clots are the leading cause of death, so doing basic research in the mechanical and elastic properties of fibrin could help us understand more about why there is a correlation between heart attack patients and stiff clots,” says Dr. Falvo.2 References

1. Murphy, S. L; Xu, J; Kochanek, K. D. National Vital Statics Report. http://www.cdc.gove/nchs/data/nvsr/nvsr60/ nvsr60_04.pdf (accessed Feb 12, 2012). 2. Interview with Michael Falvo, Ph.D. 1/26/2012. 3. Falvo, M. R; Gorkun, O. V.; Lord, S. T. Biophys. Chem. 2010, 152, 15-20. 4. Houser, J. R; Hudson, N. E; Ping, L. E; O’Brien, T.; Superfine, R; Lord, S. T; Falvo, M. R. Biophys. J. 2010, 3038-47.

Computerized organs: medical image analysis at UNC Matt Leming, Staff Writer

n 1974, UNC-Chapel Hill computer scientist Dr. Steve Pizer brought together a group of researchers to develop methods of medical image computing with one another. Today, that group does very technically difficult things such as making a 3-D interactive model of someone’s lungs or brain on a computer screen (Figure 1).

Figure 1. Early results from a Levoy volume rendering practice. Image courtesy of Dr. Stephen Pizer.

Dr. Pizer’s focus is radiation therapy, or targeting malignant cancer cells using radiation. His software generates 3-D images of organs (Figure 2) based on X-rays, sonograms and magnetic resonance images (MRIs) in addition to preprogrammed knowledge of organ Dr. Stephen Pizer shape and anatomy. “My research focuses especially on anatomic shapes and the extraction of shape information in 3-D medical imaging,” said Dr. Pizer.1 By developing a 3-D model of an organ, researchers can pinpoint the location of a tumor and focus strong radiation on a smaller area, leaving behind less damage to the surrounding normal tissue (Figure 3, left). What makes this difficult, however, is that at the time of treatment, the 3-D models are based on 2-D images. This is similar to making a detailed video game character based on a few photographs. Multiple pictures have to be taken to get an image of a lung or a kidney from different angles, and syncing those images into a sound 3-D model is a difficult task.

The UNC Medical Image Display and Analysis Group (MIDAG) has been working on this and other projects for years. A collaborative team of researchers in a number of different fields, MIDAG focuses on the analysis of medical images such as X-rays, brain scans and sonograms. “This is a collaborative project — mathematicians, statisticians, computer scientists and medical doctors have come together to work on this,” said Dr. Stephen Pizer, the head of MIDAG.1 MIDAG is a loose group. Composed of more than 90 members from various departments and spread over three medical school departments (psychiatry, radiation oncology and radiology), it is more or less centered in Sitterson Hall, UNC-Chapel Hill’s computer science department. Computer programmers there do not work directly with patients, but they develop tools used by those who do. While individuals in MIDAG work on a lot of different projects, they use similar methods to go about their work, sharing these methods with their colleagues. This collaboration is the purpose Figure 2. An early MIDAG rendition of a 3-D human lung. of MIDAG. Image courtesy of Dr. Stephen Pizer.

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Figure 3. Left: A 3-D model of blood vessels in a human brain and the tumor that they supply. Image courtesy of Dr. Stephen Pizer. Middle: Dr. Styner’s 3-D rendition of a human amygdala. Image courtesy of Dr. Martin Styner. Right: Statistical pattern recognition color-codes a functional MRI of a human brain to indicate the area of a tumor. Image courtesy of Dr. Stephen Pizer.

Other members of MIDAG, however, focus on the analysis of brain images (Figure 3, middle). Dr. Martin Styner is a member of MIDAG who boasts an office in both Sitterson Hall and the medical wing. Head of the Neuro Image Research and Analysis Laboratories, Dr. Dr. Martin Styner Styner first joined MIDAG in 1998 as a student. His research in medical image analysis has recently focused on the early development of infants. “We see how the brain develops normally,” Dr. Styner explained, “and then we see how that relates to abnormal development such as autism.”3 At his neuroimaging laboratory, Dr. Styner examines MRIs provided by other researchers who study children’s diseases. He takes brain scans from children afflicted with developmental disorders and compares them to standard brain scans to see the extent of the disorder on a biological level. The scans are done over a period of time to track their brain development as they grow older. Dr. Styner now works with a clinic that treats and studies children whose mothers were habitual cocaine users. In the Neuro Image Research and Analysis Laboratories, he examines the MRIs; in the department of computer science, he develops the tools to do this. Just as Dr. Pizer relies on knowledge of normal anatomy to make individualized 3-D models of organs, Dr. Styner compares brain scans of diseased patients to those of normal patients. This

comparison analysis of medical images is one of the key methodologies of MIDAG, and researchers in the group share different ways of doing this comparison. “Image registration is trying to align images,” said Dr. Marc Niethammer, a computer scientist of MIDAG, “and it’s one of the core pieces of a lot of medical image analysis approaches.”2 For example, if scientists were to compare brains of Alzheimer’s patients to the Dr. Marc Niethammer brains of normal subjects, they would need a method to align brain scans to spot potential differences (Figure 3, right). Of course, as Dr. Niethammer explains, the brains of two different individuals are going to be different whether or not Alzheimer’s is a factor, and these differences may be very subtle. Computer analysis is therefore necessary to quantify differences that are not explainable by normal variation. MIDAG’s research continues today, and their work holds a promising future. Whether they are researching novel methods to improve radiation therapy of cancer or examining brain scans to uncover the biological root of autism, MIDAG’s research continues to enable clinicians to better treat patients. References

1. Interview with Stephen Pizer, Ph.D. 2/1/2012. 2. Interview with Marc Niethammer, Ph.D. 2/9/2012. 3. Interview with Martin Styner, Ph.D. 2/13/2012. 4. Pizer, S. M. IEEE T. Med. Imaging 2003, 22, 2-10.

X-Raying the Skeleton of the Cell Trent Teague, Staff Writer

he interior of a cell is a chaotic scene. It constantly hums with the activity of countless chemical reactions that are churning out energy for the cell, relaying signals transmitted from outside the cell and shuttling protein products made by the cell. Yet there is order in this cellular bedlam. Microtubules, the largest component of the cell’s cytoskeleton, serve multiple purposes in the dynamics of cellular activity, and the secrets behind the dynamics of microtubules are just now starting to be fully revealed. The laboratory of Dr. Kevin Slep, an assistant professor of biology at UNC-Chapel Hill, is working to discover the factors that are at work behind the microtubule array. The implications of microtubule research have the potential to provide a new understanding

for many diseases, including the rare disorder known as Kartagener’s syndrome. This disease is a genetic disorder with a variety of symptoms; most prominently, those afflicted with the disorder possess a “mirror-image reversal of all organs.”1 For example, Dr. Kevin Slep patients with Kartagener’s syndrome have their hearts situated on the right side of their body instead of the left (Figure 1). The syndrome is believed to result from faulty cilia, small hair-like appendages composed of microtubules that are found on many cells.1 At their core, microtubules are merely polymers of a protein known as tubulin. Tubulin belongs to a class of proteins called guanosine triphosphate phosphatases (GTPases). GTPases bind the molecule guanosine triphosphate (GTP) and hydrolyze off one of its phosphate groups to form guanosine diphosphate (GDP). This hydrolysis reaction is key in regulating the dynamics of microtubule growth as only tubulin bound to GTP can be added to a growing microtubule.2 Curiously, tubulin is only added to one end of the microtubule called the “+” end; growth and depolymerization of the tubule only occur at that end (Figure 2).3 There is a whole host of proteins that have Figure 1. CT scan of a patient with Kartagener’s syndrome. been discovered recently that bind to the “+” end The heart is situated on the right (R) side of the body instead of a microtubule strand. These proteins, termed of the left (L). Anterior (A) and posterior (P) ends are also microtubule plus end-binding proteins (+TIPs), labeled.

Carolina Scientific often function as regulatory proteins for the microtubule strand. They assist in tasks such as stabilization of the microtubule and promotion of microtubule growth. The importance of +TIPs was shown in a recent experiment conducted on fruit flies (Drosophila melanogaster), where the gene controlling production of a known +TIP was deleted. The resulting mutant produced abnormal mitotic spindles.3 Researchers believe that a whole assortment of diseases in humans ranging from neurological disorders to certain cancers can be explained by a lack of functional +TIPs.3 Dr. Slep’s research primarily focuses on establishing what specific regions of +TIPs are integral in regulating microtubule dynamics. To determine what domains of the protein are relevant, it is important to first determine the structure of the protein on the molecular scale. According to Dr. Slep, oftentimes the “form of a biological molecule determines its function.”3 X-ray crystallography, a powerful imaging technique, can be used to determine a protein’s structure. When the protein is isolated within a crystal lattice, it can be bombarded with X-rays. As the X-rays collide with the atoms of the protein, they will diffract away from their initial straight path, creating a diffraction pattern that correlates with the lattice and the shape of the protein within the lattice. Diffraction intensities are measured and used to build an electron density map from which a molecular model of the protein is built (Figure 3).3

Figure 3. Schematic displaying the mechanism for X-ray crystallography. A crystallized protein is bombarded by Xrays. Diffraction patterns are formed as the X-rays diffract from regions with high electron density. A computer records the images and produces an image of the atomic structure of the protein.

Using this technique, scientists have uncovered the structure of +TIPs for several different species. Dr. Slep’s own research has shown that certain domains in +TIPs have the same conserved structure in organisms as diverse as yeast, frogs and fruit flies. That natural selection conserved the domain structure of some +TIPs across evolutionary time indicates the functional importance of these proteins.3 These conserved sites are oftentimes the site of the activity of the +TIP. For example, the +TIP family known as the TOG array contains a domain that is shown to interact with the “+” end of a microtubule strand and is believed to stabilize the microtubule. Mutations can be induced that alter the structure of this domain. The microtubules of cells that possess the mutation lack the stability found in normal cells and struggle to maintain tubule polymerization.4 The ability to determine the function of +TIPs by deciphering their structure represents a common theme in biology. The implications of the Slep laboratory’s research could give rise to a newer and more thorough understanding of the diseases that result from malfunctioning microtubules. This could in turn give way to finding therapies for disorders like Kartagener’s syndrome at the genomic level, with the potential to cure such diseases rather than simply treat their effects. References

Figure 2. Image detailing the growth of the microtubule array in a cell. The image is artificially colored to display the “+” end of the microtubules, which appear green in the image. Image courtesy of Dr. Kevin Slep.

1. National Institutes of Health. Kartagener Syndrome. http://www.rarediseases.info.nih.gov/GARD/QnASelected. aspx?diseaseID=6815 (accessed Feb 22, 2012). 2. Slep, K. C. Biochem. Soc. Trans. 2009, 37, 1002-1006. 3. Interview with Kevin C. Slep, Ph.D. 1/20/2012. 4. Slep, K. C. Structural Mechanisms for Regulating Microtubule Dynamics. PowerPoint presentation.

mother can pass on many things to her chil- that “this story really begins dren — the color of her eyes, the curliness of before the date of birth.”2 her hair and even her predisposition to certain While long-term evodiseases. All of these things are genetic traits that lutionary genetic changes are beyond her control. However, current research give us a background for how suggests that some aspects of a child’s develop- genes can potentially function, ment may be affected by something that is under epigenetics explains the shorta mother’s control — her diet. Dr. Mihai Niculescu, term mechanism for how en- Dr. Mihai Niculescu assistant professor at the UNC Nutrition Research vironmental pressures affect Institute (NRI), is studying how maternal nutrition the genome.2 Epigenetics is the study of changes may affect fetal brain development through epi- in gene expression that don’t involve changes in genetic inheritance. DNA sequence.2 The most common type of epiDr. Niculescu’s research is based on the idea genetic change is DNA methylation, in which a that characteristics acquired through environ- methyl group (–CH3) is added to the promoter mental influences such as nutrition can be inher- region of a gene. The addition of methyl groups ited. According to evolution, an individual forms causes the promoter to be less accessible to tranphysiological adaptations to the nutrient avail- scription factors, leading to less gene activation. ability in its environment.1 For example, if a moth- Because the DNA of sperm and ova has specific er’s diet consists of high-fat food, her child will be methylation patterns, children can inherit epi“instructed” in the genetic changes and womb that this is the their associated phemost available food notypes from their in nature and will be parents.1 primed to search for Dr. Niculescu this food. The materis particularly internal signals received ested in studying by the child during how certain physifetal development ological adaptations allow it to adapt to triggered by mathe predicted outside ternal nutrition are environment. Thus, heritable through while many factors epigenetic mechamay affect the diet nisms. Currently, he of an individual, Dr. Figure 1. Illustration of DNA methylation. Image courtesy of Dr. is researching how Niculescu believes Mihai Niculescu. “omega-3 fatty acids

Carolina Scientific may epigenetically alter the association between maternal obesity and post-natal brain development.”2 Omega-3 fatty acids are known to be essential to fetal and postnatal brain development.3 A manuscript that Dr. Niculescu is currently preparing shows that a deficiency in omega-3 fatty acids causes a decrease in DNA methylation of the FADS2 gene, which is responsible for converting α-linolenic acid (ALA) to docosahexaenoic acid (DHA).2 A decrease in methylation results in greater activation of the FADS2 gene. In a recent study, Dr. Niculescu looked at whether the maternal availability of ALA altered hippocampal development of mice during the gestation and lactation periods. His experiment involved four groups of mother mice that were given varying amounts of ALA in their diet during gestation and lactation. The offspring’s brains were then analyzed to determine the effect of their mothers’ nutritional availabilities. The results Figure 2. The brains of the mice offspring were sectioned for immushowed that while ALA supplementation nohistochemistry assessment in (a) cell proliferation, (b) apoptosis during lactation enhanced the offspring’s and (c) early neuronal differentiation. (d) Representative images are neurogenesis, or birth of brain cells, its presented, and white arrows indicate the presence of positively labeled beneficial effects were offset by ALA defi- cells. Image courtesy of Dr. Mihai Niculescu. ciency during the gestational period. Thus, it was teractions may be as important as an individual’s concluded that in order to enhance brain devel- genetic background. Thus, our traditional idea of opment, ALA is required during both the fetal and the food guide pyramid as the ideal healthy diet postnatal stages of brain development.3 may not be true anymore. Instead, our individual In addition to this study, Dr. Niculescu, in col- nutrient requirements must be determined by laboration with Dr. Carol Cheatham of the NRI, is looking at our genomes from both a genetic and currently conducting an experiment to see if flax- epigenetic perspective. By screening individuals seed oil supplements, which contain high levels for their genetic and epigenetic patterns, those of ALA, enhance the learning abilities of human who are at risk for certain health conditions can toddlers.2 In this experiment, toddlers were given be identified, and prevention policies can be tareither an ALA supplement or a placebo for three geted toward them.2 In the future, Dr. Niculescu, months. Baseline assessments of their cognitive in collaboration with his colleagues at NRI, hopes abilities at the beginning of this study will be com- to “develop a unifying theory that would allow us pared to those conducted at the end. So far, it has to find their individualized nutrient requirements been observed that the children of mothers who based on genetic and epigenetic differences,”2 have a genetic deficiency in FADS2 perform worse revolutionizing nutrition as we know it today. on the cognitive tests. This suggests that taking omega-3 supplements during gestation may have References 1. Niculescu, M.D. Synesis: A Journal of Science, Technology, a role in improving the cognition of children.2 Ethics and Policy. 2011, G, 18-26. According to Dr. Niculescu, the fact that 2. Interview with Mihai D. Niculescu, M.D., Ph.D. 2/2/2012. maternal nutrition induces heritable DNA meth- 3. Niculescu. M. D.; Lupu, D. S.; Craciunescu, C. N. Int. J. ylation changes suggests that gene-nutrient in- Dev. Neurosci. 2011, 29, 795-802.

We Are Small But Mighty Microbial Life at the Bottom of the Sea Kelsey Ellis, Staff Writer

t doesn’t take long — two hours, at the most — to reach the bottom of the world.1 As the tiny submersible Alvin, crowded with only two observers and a pilot, traverses the topography of the seafloor, the loneliness of its lights in the darkness can be compared to that of a space shuttle lost in the vastness of space (Figure 1). Much is still unknown about the seafloor and the organisms that reside there. For researchers such as Dr. Andreas Teske, who specializes in the microbiology of deep sea sediments, this means that the world of the deep ocean is full of the possibility of new discoveries. Dr. Teske sees the potential of a world full of microbes. Bacteria and archaea come in a wide

range of forms, from small bacteria to (comparatively) giant microbial mats found at marine hydrothermal vents that have filaments several centimeters long and are thicker than human hair (Figure 3).1 For Dr. Teske, it is the “metabolic and biochemical variety in microor- Dr. Andreas Teske ganisms” that he finds fascinating as well as the challenge inherent in doing research on a group of organisms that live in conditions that would kill most other life forms. While microbes encompass such diverse organisms as viruses and fungi, Dr. Teske’s research focuses on the bacteria and

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Figure 1. The submersible Alvin aboard its mother ship, RV Atlantis. Image scourtesy of Dr. Andreas Teske.

archaea of deep marine sediments and hydrothermal vents. These microbes do not need oxygen to survive like humans do. Instead, they use anaerobic respiration, which is a different metabolic pathway that generates energy in the absence of oxygen. Different groups of microbes utilize different chemicals. Some respire with sulfate and produce sulfide, and others produce methane from carbon dioxide and hydrogen through methanogenesis.2 As part of his research, Dr. Teske travels first by research vessel and then by submersible to environments such as the hydrothermal vents of Guaymas Basin, near Baja California. These vents in the ocean floor spew superheated water, methane, carbon dioxide, sulfide and other chemicals from the sediment into the water column.3 He has also gone on research cruises to the Gulf of Mexico to examine microbial communities at active mud volcanoes and brine pools.2 Mud volcanoes on the seafloor discharge large Figure 2. A map of Guaymas Basin, near Baja California. Adapted amounts of fluidfrom a USGS shaded relief map. ized gas and mud,

while brine pools are puddles of denser water that form on the seafloor. The fluid in a brine pool remains separate from the surrounding water because of its high salt concentration, which makes it denser, so it stays at the sediment surface. The microbial community structure at these extreme habitats is important, says Dr. Teske, because these organisms are one of the many microbial groups that together â&#x20AC;&#x153;catalyze the biogeochemical cycles of planet Earth. Without the constantly churning microorganisms as the chemical engines, life on Earth would come to a standstill.â&#x20AC;? Microbes can take credit for the invention of photosynthesis, which converts carbon dioxide and light energy to oxygen and organic matter. They also help to turn atmospheric nitrogen into bioavailable forms to keep it available for other organisms.1 These microbial duties may seem distant and irrelevant deep under the oceanâ&#x20AC;&#x2122;s surface, where the water pressure reaches levels intolerable to any organism from the surface biosphere. But in the darkness, bacteria provide similar services to the benthic, or bottom, ecosystem as their relatives do to shallow-water and terrestrial systems. By utilizing the energy-rich chemicals and nutrients extruded into the water at mud volcanoes and hydrothermal vents in a process called chemosynthesis, deep sea bacteria and archaea take the place of photosynthesizing plants. They help to form the base for a deep sea food web, stretching from benthic invertebrates up to fishes, that would otherwise not exist.1 Dr. Teske has also collected sediment core samples from multiple

sites that show that microbial activity continues deep into the subsurface of mud volcanoes and hydrothermal vents (Figure 4). This means that these microbes are also serving to link the ocean bottom habitat with that of the deep subsurface.2 While the microbes that are the subject of Dr. Teske’s research are able to thrive in extremely inhospitable environments, another carefully documented characteristic is their sensitivity to variations in “fluid composition and flow regimes, temperature, substrate concentrations, competition with other organisms and salinity.”2 Microbes that live at Guaymas Basin hydrothermal vents are subject not only to geochemical variables but also to a temperature gradient that goes from Figure 4. Hydrothermal vent sediment cores from a re2-20 °C at the sediment-water interface to greater search cruise to Guaymas Basin. Image courtesy of Dr. Andreas Teske. than 100 °C at 30 cm sediment depth.3 Dr. Teske discovered evidence of anaerobic oxidation of different microbial assemblages occupied the methane carried out by microbial communities sites. While the bacteria at the brine pool showed even over this temperature gradient. A challenge high rates of sulfate and acetate production, in Dr. Teske’s research is to those at the mud volcano separate the effects of each “Without the constantly churning had high rates of methane of these variables from one microorganisms as the chemical engines, production. Other factors, another in order to see how such as differences in input life on Earth would come to a each individually affects miof dissolved organic matter standstill.” crobial communities. and rates of fluid advection, Even environments create completely different that initially seem similar can harbor very differ- microbial communities at these sites. ent bacterial populations. Dr. Teske recently inWhile we are used to thinking of our oceans vestigated the microbes living at an active mud as being filled with whales, fish and the occasionvolcano and a brine pool on the seafloor of the al marooned sailor, in reality it is the microscopic Gulf of Mexico. Through genetic analysis, he dis- organisms such as bacteria that are the true drivcovered that though these two environments are ers of biogeochemical processes. As humans, we anoxic, or oxygen-deficient, and hypersaline, very benefit indirectly from their ability to sequester carbon and sustain marine food webs in the lightfilled surface waters as well as in the deepest seas. Yet even though these organisms play a huge role in ocean function, “the microbial biosphere is full of organisms that at present are uncultured — we don’t know what they are actually doing.”1 It is the job of scientists such as Dr. Teske to explore these extreme environments and to further our knowledge of the organisms that live there. References

Figure 3. Orange and white mats of large, sulfur-oxidizing chemosynthetic Beggiatoa spp. near a hydrothermal vent in Guaymas Basin. Image courtesy of Dr. Andreas Teske.

1. Interview with Andreas Teske, Ph.D. 1/27/2012. 2. Joye, S. B.; Samarkin, V. A.; Orcutt, B. N.; MacDonald, I. R.; Hinrichs, K. U.; Elvert, M.; Teske, A. P.; Lloyd, K. G.; Lever, M. A.; Montoya, J. P.; et al. N. Geo. 2009, 2, 349-354. 3. Biddle, J. F.; Cardman, Z.; Mendlovitz, H;. Albert, D. B.; Lloyd, K. G.; Boetius, A.; Teske, A. ISME J. 2011, 1-14.

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Hetali Lodaya, Staff Writer

tudies like HPTN 052 involve a lot of waiting. thought the study had failed.”1 The National Institutes of Health-funded Rather, the researchers were stunned to hear investigation led by UNC School of Medicine’s Dr. that the data was so compelling that they were in Myron Cohen explores the idea that proper use fact being advised to release it early. HIV causes of antiretroviral drugs (ARVs) as a treatment for a long-term infection that eventually leads to human immunodeficiency virus (HIV) can decrease acquired immune deficiency syndrome (AIDS), in infectiousness and therefore which a patient is susceptible help prevent the transmission to even minor infections that 1 of HIV from an infected person. would not be fatal to the rest The ten-year study began in of the population. The HIV2005 and enrolled more than AIDS epidemic is rampant, with 1,700 couples worldwide. It the World Health Organization is a double-blind study, so estimating more than 33 neither the researchers nor million cases across the world.3 the patients know who is Current treatments address receiving treatment; the data symptoms or attempt to slow is monitored periodically progression of the disease from by an outside review board HIV to AIDS. Named Science that assesses progress, offers magazine’s Breakthrough of recommendations on the study the Year (Figure 1), the finding design and very rarely suggests that ARVs decreased the risk changes to a study’s timeline. of heterosexual transmission At an annual review meeting of the disease by 96 percent Figure 1. Cover of December 2011 Science last April, when unexpectedly finally offers a preventative magazine announcing Dr. Cohen’s asked to leave the room and study as Breakthrough of the Year. measure against HIV and is return again, Dr. Cohen’s Image courtesy of Thomas Deerinck, a game-changer for future research team feared the worst. Kathleen Fitzpatrick, John Guatelli, and research, policy initiatives and Mark Ellisman, NCMIR, UCSD/Visuals “No one made eye contact. We those who live with the disease. Unlimited, Inc.

HIV has been difficult to treat in part because it affects every person differently.3 The infection works by damaging the body’s CD4+ T cells, which are crucial for fighting infectious diseases (Figure 2). Sometimes flulike symptoms show immediately upon infection with HIV, but it can go undetected for years as the body’s capacity to resist disease slowly wears down. Indeed, the five men first diagnosed with HIV-AIDS were identified because they all developed Kaposi’s sarcoma, a rare cancer that would not normally appear in any population with that level of prevalence. It is these different acquired diseases that generally lead to the death of Figure 2. Electron microscope capture of HIV cells, seen as dots on a those with HIV-AIDS.4 HIV is known to spread in several white blood cell. HIV works by damaging a type of white blood cell, CD4+ ways, all involving exposure to bodily T cells, making the body more susceptible to infection. Image from the CDC/C. Goldsmith, P. Feorino, E. L. Palmer, and W. R. McManus. fluids from an infected person, such as having unprotected sex or sharing needles. At the beginning of the AIDS epidemic, is designed to be long-term, comprehensive and patients could expect to live for about one to conclusive to settle the debate once and for all.5 “Discordant” couples, in which one partner was known to be infected with HIV but had not yet progressed to the AIDS stage and the other partner was HIVthree years after negative, were enrolled in the study and divided contracting HIV. into two groups. Half of the infected patients There is currently were given ARVs right away, while the rest were no way to rid given treatment once their body’s CD4+ T cell the body of HIV; Dr. Myron Cohen however, since the introduction of ARVs, patients have seen drastic increases in life expectancy with proper treatment and monitoring. The goal of the HPTN 052 study is to address a claim gaining traction in the medical community: If ARVs decrease HIV levels in the body, individuals taking ARVs should be less infectious. It is a controversial question to even ask — many researchers and health officials fear that the idea that taking ARVs makes a patient less infectious will cause high-risk individuals Figure 3. Transmission electron microscopy image to ignore established health policy regarding of HIV virus cells. Image from the CDC/Dr. Edwin P. Ewing, Jr. protected sex and sharing of needles. The study

Carolina Scientific counts dropped to levels at which the WHO recommends beginning treatment. Partners were routinely tested to see if there was a difference in HIV transmission rates between the group taking ARVs and the group not on the medication. That the study results were released so early indicates the magnitude of the findings: Of the 28 people in the entire study who contracted HIV from their infected partners, only one had a partner taking ARVs. Of the early treatment group, 41 percent of patients also experienced fewer side effects. No unexpected or unmanageable side effects were noted, allowing the researchers to be confident that only one variable was being manipulated — the presence or absence of ARVs in patients’ bodies. “This study was predicated

on biological plausibility,” stresses Dr. Cohen. “The drugs for treatment were chosen based on previous studies conducted to prove their efficacy and to prove that they were right for this study.” While these findings emphasize individual benefits, the next step is to conduct a population study to show whether this method of prevention works on a large scale. According to Dr. Cohen, “If people take their pills, we expect to see a benefit.” With a small study like HPTN 052 being managed at clinics like the one shown in Figure 4, it is much easier to ensure compliance with medication regimens. Next, HPTN 071, a population level study that will enroll over 1.2 million participants, will help researchers understand what happens with this strategy on a large scale.1 As we enter the 31st year of the HIV pandemic, this discovery is not a magic bullet-the ultimate research goals are still an HIV vaccine to prevent infection and a cure for those already infected. It gives support, however, to the current policy of increasing ARV availability and creating costeffective systems to treat all patients in order to get the most improvement possible out of early treatment regimens. If the combination of ARV therapy and protective measures such as condom

use can decrease transmission of HIV to a new population, the world might move one step closer to what Secretary of State Hillary Clinton has called “an AIDS-free generation.”6 Dr. Cohen notes, though, that “from an investigator’s point of view, this really isn’t over. It’s not about the end — it’s about the journey we take to get there.”

Figure 4. AIDS clinic in Himachal Pradesh, India. Treatment and education centers such as these are essential to decreasing transmission rates. Image by John Hill, [CC-BY-SA-3.0].

References

1. Interview with Myron S. Cohen, M.D. 3/2/2012. 2. Cohen, J. Science 2011, 334, 1628. 3. Centers for Disease Control and Prevention. Basic Information About HIV and AIDS. http://www.cdc.gov/hiv/ default.htm (accessed Mar 24, 2012). 4. World Health Organization. HIV/AIDS. http://www. who.int/hiv/topics/en/ (accessed Mar 24, 2012). 5. Rogers, C. HPTN 052 Named Top Scientific Breakthrough of 2011, 2011. HIV Prevention Trials Network. http://www.hptn.org/web%20documents/IndexDocs/05 2NamedScientificBreakthrough2011.pdf (accessed Mar 24, 2012). 6. Stein, R. Hillary Clinton Calls for “AIDS-free Generation” The Washington Post [Online], Nov 8, 2011. http://www. washingtonpost.com/national/health-science/hillary-clinton-calls-for-aids-free-generation/2011/11/08/gIQA6LjF1M_ story.html (accessed Mar 24, 2012).

Growing Pains

Dylan Campfield, Staff Writer

Research on the Warburg effect could help explain how what you eat causes changes deep inside of your cells — changes that might lead to a deadly disease.

o one likes cancer. Fortunately, UNC-Chapel Hill has always aimed at raising money, raising awareness and conducting research to further the understanding and prevention of cancer. The latter happens to be Dr. Dallas Donohoe’s forte. One of Dr. Donohoe’s current research topics is the Warburg effect, the act of a cancerous cell switching to an alternative method of energy metabolism. Dr. Donohoe has used a short fatty acid chain called butyrate to probe how the Warburg effect can lead to altered gene expression in a cancer cell (Figure 1).1 Butyrate is a naturally occurring compound that is produced in the colon

Figure 1. In the absence of the Warburg effect, butyrate no longer increases histone acetylation at lower doses, shown in this Western blot. Image courtesy of Dr. Dallas Donohoe.

and derived from the gut microbiota and dietary fiber that is consumed. Our own host cells cannot metabolize the fiber, but bacteria do. When they ferment, the fiber butyrate is produced. It plays a role in gene expression and functions as the primary energy source for colonocytes, the cells that form the lining of the colon.2 Dr. Donohoe notes that mice without bacteria do not produce butyrate.1 In the colon, colonocytes have evolved to utilize butyrate as their major energy source. The use of butyrate is the major difference between a

cancerous and non-cancerous colonocyte. The Warburg effect is the actual process of cancerous cells converting to glucose metabolism over butyrate. The cancer cells become increasingly reliant on glucose and can increase one hundredfold the amount they take in by up-regulat-

“The Warburg effect is found in the majority of cancers, almost 90 percent.” ing glucose transporters.1 Using a glucose analog (a separate entity performing similar functions) and positron emission tomography (PET) imaging, researchers can detect the accumulation of glucose to see exactly where in the body cancer is forming. “What I have been able to work out,” Dr. Donohoe states, “is [that] in the Warburg effect, butyrate no longer metabolizes because it is not needed any longer and will therefore accumulate in the cell. Accumulation leads to a different action altogether, where it can go to the nucleus and modify histones Figure 2. Skeleton structure that control gene of butyrate, the conjugate base of butanoic acid. expression in the cell.”1 Without the Warburg effect, butyrate no longer increases histone acetylation (Figure 2). Reduced histone acetylation directs the cell to kill itself through apoptosis, or programmed cell death (Figure 3). Nobel Prize winner Dr. Otto Warburg first no-

Carolina Scientific ticed this difference in cancer cell energy production, which was later called the Warburg effect. The cancer cell uses aerobic glycolysis instead of oxidative metabolism to produce 2 adenosine triphosphates (ATPs) instead of 36. This seems like a strange way to produce ATP when a cell can efficiently produce ATP by oxidative metabolism, but a cancer cell also takes up much more glucose. Dr. Donohoe explains that if a normal cell takes up 10 molecules of glucose, cancer cells would take up 10 times that much. This excess glucose is used to compensate for the energy expenditure and is also used as a carbon source to help double its biomass during replication.1 “The Warburg effect is found in the majority of cancers, almost 90 percent,” Dr. Donohoe reveals.1 Comparatively, defects and mutations in tumor suppressor genes, such as p53, are only found in approximately 50 percent of cancers. However, the Warburg effect has gone mainly unnoticed. “In the 1970s, scientists discarded the Warburg effect, still wondering how to make sense of the 10 percent of cancers that it doesn’t explain,” Donohoe states. “Today, we’re seeing a re-emergence of interest in the Warburg effect.”1 In his laboratory, Dr. Donohoe implements various biochemical techniques that explore the Warburg effect. RNA interference has been shown to be one of the more useful tools. Dr. Donohoe

Figure 3. A cluster of cancer cells undergoing apoptosis. Image by Amy Dame, [CC-BY-NC-ND 2.0].

Figure 4. Cancerous human colon cells. Image by Annie Cavanaugh, [CC-BY-NC-ND-2.0].

an integral component in butyrate’s mechanism for mediating histone acetylation. Dr. Donohoe also implements liquid chromatography mass spectrometry (LC/MS-MS) to measure isotope-labeled or endogenous butyrate levels in the cell. Accumulation of butyrate indicates that the cell is no longer completely utilized for energy. Dr. Donohoe can inject a cell lysate into the LC/MS-MS instrument and identify butyrate based on its molecular weight.1

UNC-Chapel Hill has always aimed at raising money, raising awareness, and conducting research to further the understanding and prevention of cancer. Dr. Donohoe wishes to use his research on the Warburg effect to better understand how diet and nutrition give rise to changes in epigenetics that in turn regulate gene expression and cellular phenotype. “People realize by changing their diet, you can alter gene expression, but how is this happening? How is it regulated?”1 Through a better understanding of the interplay between diet, metabolism and epigenetics, Dr. Donohoe seems hopeful that researchers can find a link between diet and nutrition and cancer development. References

1. Interview with Dallas R. Donohoe, Ph.D. 2/10/2012.

uses complementary RNA to bind ATP citrate ly- 2. Donohoe, D.; Garge, N.; Zhang, X.; Sun, W.; O’Connell, ase mRNA, which leads to transcript degradation T. M.; Bunger, M. K.; Bultman, S. J. Cell Metab. 2011, 13, and diminished protein levels. ATP citrate lyase is 517-526.

A Dynamo in the Brain Bhavesh Patel, Staff Writer

he brain is a dynamic and sensitive organ. It has the ability to store massive amounts of knowledge, process information instantaneously and command the entire human body, yet it is sensitive enough to notice changes in pH, nutrients and even external disturbances such as loud noises and vibrations. Thus, it would make sense that the cells maintaining brain homeostasis are equally dynamic. Microglia are specialized macrophage cells located in the central nervous system.1 The generalized function of these cells is to maintain homeostasis in the brain, yet the exact mechanism of how they operate and how they are produced is still being researched. At UNC-Chapel Hill, Dr. Glenn Matsushima in the department of microbiology and immunology has made great strides in understanding microglial cells. Dr. Matsushimaâ&#x20AC;&#x2122;s laboratory studies microglial response to disease and injury in the brain. A substantial issue with studying microglia is that it is not clear what causes changes in microglial cell function over time during moments of distress. Dr. Matsushima states, â&#x20AC;&#x153;My

Figure 1. Microglial clearing of cell debris is critical for remyelination to occur. Image courtesy of Dr. Glenn Matsushima.

Dr. Glenn Matsushima has had a long-standing interest in neuroimmunology and believes that his current research will be applicable to other neurologic diseases where microglial responses are prominent.

belief is that in general, the microglia have a basic assigned function to them, and if we can discover what they do and understand how they do it, it could be applicable to other types of insults, brain injuries and diseases.â&#x20AC;?2 One of the diseases he is targeting is multiple sclerosis. Multiple sclerosis is a complicated autoimmune disease that targets the myelin in the central nervous system.1 Dr. Matsushima replicates symptoms of multiple sclerosis in the brain of mice by using an artificial neurotoxicant that targets the cells that form the myelin around nerves. This model was chosen because it accurately mimics a progressive stage of multiple sclerosis that signals a robust response from microglia but a less active response from other immune cells. Microglial cells exhibit both stationary and mobile characteristics. Studies have shown that under normal circumstances, microglia are stationary, extruding branches to nearby neurons and other glial cells. When a cell in its region is disturbed, the microglial cells are activated and retract their extensions, becoming more amoeboid in nature. A large number of microglial cells then converge on the area under distress.1 Dr. Matsushima and a close UNC-Chapel Hill collaborator, Dr. Jenny Ting, noticed that the microglia generally perform two functions during an immune response. At first, they converge to the affected area and act as bulldozers, clearing away dead cells and cell debris. While they are clearing the unwanted debris, the microglial cells

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Figure 2. Microglia accumulate in regions of demyelination and aid in repair. As the region is repaired, migrolia begin to leave the area. Image courtesy of Dr. Glenn Matsushima.

perform a second reparative function by secreting Although it is unknown how efficiently growth factors and cytokines such as tumor these microglial cells replace the old ones, it has necrosis factor alpha (TNF-Îą). These secretions been noted that with continued injury, there is signal precursor cells to come to the damaged less recruitment and response from microglial area and to begin differentiating in order to cells. This is thought to be a large reason for the replace the lost cells as well as to recruit other difficult recovery from late stages of multiple glial cells for repair. The clearing away of debris sclerosis. During early stages of multiple sclerosis, is very important to this the microglial response process as the dead cell is rapid and efficient debris has been noted enough to repair the to inhibit differentiation damage; however, as of precursor cells (Figure the disease progresses, 1). the response and repair In multiple sclebecome less efficient, rosis, lesions of demyleading to worsened elinated nerves appear lesions. Eventually the randomly in the brain. repair mechanisms These lesions activate stop all together, and microglial response, and the lesions become the impaired cells are Figure 3. Graphical representation of microglial response permanent.2 removed. The microg- to demyelination. Microglial response increases as soon Dr. Matsushima lia then signal precur- as demyelination begins and peaks when re-myelination points out that if new begins. Image courtesy of Dr. Glenn Matsushima. sor cells for the repair of precursor cells are these lesions. Multiple sclerosis patients can have introduced to the affected area in his animal multiple lesions at any one time, all of which are model, repair can continue, which makes the case repaired simultaneously during the early stages that during progressive stages, it is not a repair of the disease. issue but rather a recruitment issue. If this issue Dr. Matsushima believes that the recruitment can be addressed, there could be a chance to function of microglia triggers the long-term repair stop the harmful progression of multiple sclerosis that is carried out by astrocytes. The microglial cells into irreparable stages. Dr. Matsushima believes jumpstart the clearing and repair, but the majority that multiple sclerosis and other degenerative of repair is then handed off to the astrocytes. After diseases could be treated more effectively with handing off the repairing responsibilities to the further understanding of microglial function. astrocytes, some of the microglia return to their original location while others are sacrificed and References recycled to make way for new microglial cells.2 1. Saijo, K.; Glass, C. K. Nat. Rev. Immunol. 2011, 11, 775-787. This response is shown in Figure 2 and Figure 3. 2. Interview with Glenn Matsushima, Ph.D. 2/1/2012.

G R O I

R I GH T D I R E C TI O N Wylder Fondaw, Staff Writer

he threat of a lifelong genital herpes infection is skin through which virus paralarming to college students everywhere. With ticles can enter the patient; one out of every six 14- to 49-year-old individu- thus, “[patients infected] with als in the United States testing positive for genital HSV-2 have an elevated risk of herpes, it is clear that the risk of acquiring herpes contracting HIV.”4 While there is a widespread problem.1 In addition, there has is disagreement about the exbeen a marked increase in herpes cases since the tent to which HSV affects HIV early 1970s (Figure 1). Thankfully, UNC-Chapel contraction, some estimates Dr. Peter Leone Hill’s very own Dr. Peter Leone, a professor at both predict 200 to 300 percent inthe School of Medicine and the Gillings School of crease in the likelihood of HIV contraction for indiGlobal Public Health, has been researching her- viduals infected with HSV.2 pes simplex viruses 1 and 2 (HSV-1 and HSV-2) to Fortunately, researchers across the country find a cure for the prevalent sexually transmitted are investigating ways to cure the virus, and Dr. disease. Leone’s research is at the forefront. This first protoGenital herpes is a sexually transmitted dis- type vaccine, named gD-2 for the protein particles ease caused by either HSV-1 or HSV-2 but usually used in its creation (Figure 3), was recently tested by the latter. While HSV-1 is typically responsible at St. Louis University in Missouri, which, as Dr. Lefor oral lesions, it can also cause a comparatively one points out with a reserved smile, is a conservaless severe case of genital herpes. Herpes usually tive Jesuit institute. After eight years of research, transmits through skin-to-skin contact. After an gD-2 entered phase III trials, the last round of clinioften mild initial outbreak, herpes enters a latent phase during which it can hide in the host’s nervous system without any sign of infection for years before activating. Once activated, however, HSV causes recurrent oral or genital lesions, depending on the infection’s location. The strain of HSV is not the only determinant of oral or genital herpes. Sometimes HSV-1 is responsible for genital herpes infections, but these infections are generally associated with less Figure 1. Graph of HSV prevalence that shows how HSV is a long-term disease frequent breakouts. Herpes le- that is endemic to the United States. Image from the Centers for Disease Consions are vulnerable holes in the trol and Prevention.

Carolina Scientific cal trials, in late 2011. But after so much promise, Dr. Leone was “very disappointed” when the vaccine was “only minimally effective for HSV-1 [and] showed no significant protection against HSV-2.”4 Seemingly, in attempting to make a vaccine for HSV-2 genital herpes infections, the researchers had created a potential cure for HSV-1. As for this chanced-upon vaccine for HSV-1, Dr. Leone has little hope of its being a feasible drug since “HSV-2 is more common [in genital in- Figure 2. Chronological stages of progression from contraction to infection of HIV. fections] … [and has] a much Image courtesy of Dr. Peter Leone. higher risk factor for fetal transmission and for acquiring HIV.”4 Indeed, cre- to protect against HSV. Work has been done with ating an HSV-1 vaccine was never Dr. Leone’s in- live HSV vaccines before, but with the failure of tent. Although an HSV-1 vaccine sounds wonder- protein vaccines now apparent, there will likely be ful to those who struggle with annoying cold-sore an increased focus on live vaccines in the future. outbreaks, a vaccine must provide substantial While there is more risk and red-tape associated protection against HSV-1 and 2 before it can be with a living vaccine, Dr. Leone agrees that living subjected to more intensive testing. vaccines should be the focus of HSV vaccine reThere may not be a new vaccine for herpes search. on the shelf as soon as hoped for, but the foundations for the next round of research have been made. Soon after the gD-2 trial, Dr. Leone told the New York Times, “The failure of the vaccine really suggests that we need to look at new approaches to HSV vaccine development.”3 The gD-2 vaccine consists of a piece of the herpes virus’s outer membrane named the gD protein. Upon vaccination, the immune system builds a defense against the virus by making antibodies against the gD protein Figure 3. HSV viral anatomy that shows the (Figure 3). The protein vaccine “had seen promisprotein structures of gD-2 used in the vaccine. ing results in women during our earlier trials.”4 Dr. Image courtesy of Dr. Peter Leone. Leone notes that the success of the research was learning more about the virus. “This is why we do References trials,” Dr. Leone further points out.4 Although Dr. Leone was disappointed with 1. Centers for Disease Control (CDC). STD Facts — Genital the results of the vaccine trials, it is worth not- Herpes. http://www.cdc.gov/std/herpes/stdfact-herpes. ing that that HSV-1 and 2 are nearly identical and htm (accessed Feb 5 2012). even have very similar DNA. In fact, gD-2’s ineffec- 2. Looker, K. J.; Garnett G. P.; Schmid G. P. Bull. W. H. O. tiveness is still something of a mystery. Dr. Leone 2008, 86, 805-812. 3. Bakalar, Nicholas. Prevention: Herpes Vaccine Falls Short suspects that instead of inducing anti-HSV anti- in Clinical Trial. The New York Times, New York, Jan. 10, bodies to develop immunity, future HSV vaccine 2012, D6. research will focus on using entire virus particles 4. Interview with Peter Leone, M.D. 1/30/2012.

Humanized Mice Accurately Mirror the Human Immune Response to HIV Infection Olivia Snyder, Staff Writer

ooking at a furry, white mouse nibbling at its food in the laboratory of Dr. J. Victor GarciaMartinez, it might be hard to imagine that there would be any similarities between a human being and this small animal. The reality, however, is astounding. Pioneering research led by Dr. Garcia’s laboratory at UNC-Chapel Hill has resulted in the development of a humanized mouse model that possesses a fully functioning human immune system, complete with an array of human immune cells as well as a human thymus.1 The creation and subsequent validation of this model as an accurate depiction of human immune responses have facilitated the investigation of a multitude of serious illnesses, including infection by the human immunodeficiency virus (HIV) — the causative agent of acquired immune deficiency syndrome (AIDS).2

Figure 1. A reproduction of the human thymus as seen in Gray’s Anatomy. The thymus is where the body’s immune cells learn to distinguish native cells from invading foreign cells.

Central to the motivation to produce a model are the ethical problems raised by performing research on humans.2 Furthermore, when humans are involved, the researcher lacks control over key aspects such as how the individuals Dr. J. Victor were infected, what strain of vi- Garcia-Martinez rus they are infected with and whether comorbidities are present.2 As Dr. Garcia explains, “When you use animal models, you have a great deal of control over everything you do. … You know when you are going to infect it, you know when you are going to administer therapy … you control everything.”2 Consequently, researchers have turned their attention towards the creation of a nonhuman model that can mimic key aspects of the human im- Figure 2. HIV shown budmune system. The cre- ding out of a T cell, the ation of a humanized immune cell most commonly mouse model is an el- targeted by the virus. Image from the National Institutes egant manner in which of Health/Department of HIV studies can be con- Health and Human Services. ducted in vivo. Using humanized mice also enables researchers to test various drug therapies using the exact medications currently prescribed to human patients. As the name suggests, a mouse model of the human immune system is only an imitation of the genuine article. Though not every aspect of the human immune system can be replicated in a

Carolina Scientific mouse, Dr. Garciaâ&#x20AC;&#x2122;s laboratory has, through the de- system to seek out and destroy latently infected velopment of the bone marrow, liver and thymus cells as they are not producing viral proteins.2 The (BLT) mouse, created a model that displays the generation of HIV latency in humans remains one critical features of a functionof the greatest hurdles still ing immune system.1 Perhaps to be overcome in the fight the most significant feature of against this epidemic. In order the BLT model is the presence for the BLT mouse model to 1 of a bona fide human thymus. be an effective research tool, This tissue, which stems from it must be capable of generatan implanted piece of human ing latent HIV. thymic tissue, develops into To determine whether a functional thymus capable BLT mice are capable of proof educating the developing ducing HIV latency, mice were T cells in the same manner infected with HIV-1 and then found in humans (Figure 1).1 started on ART.3 Their viral Since T cells are the immune load was calculated by samcells targeted by HIV, having pling their plasma and then true human T cells present in determining the amount of vithe mouse model is critical ral RNA present in the sample.3 (Figure 2). However, even with Within eleven days, the viral a functional human thymus, load diminished to below dequestions remain regarding tectable levels.3 Subsequent how accurately HIV infection discontinuation of ART led to in a humanized mouse mirrors an increase in viral RNA in the infection in humans. tissues and peripheral blood, One key difference besuggesting the presence of tween HIV and other viruses is latent HIV.3 Postmortem tissue that it is a retrovirus (Figure 3).2 analysis revealed the presThe genetic material of a retroence of latently infected cells virus is made up of RNA, which in these mice, consistent with is then transcribed into DNA what one would expect to using virus-encoded proteins. find in humans.3 This characteristic has served Figure 3. The life cycle and process of repThis recent study, demlication displayed by HIV. This pattern is well in creating highly efficaonstrating that humanized cious interventions such as common to all retroviruses. Image by Mark BLT mice are capable of gen2 Pellegrini, [GDFL]. antiretroviral therapy (ART). erating latent HIV, opens ART lowers the amount of viral RNA present in a many doors for the continued study of HIV using patientâ&#x20AC;&#x2122;s system, restoring immune function and humanized mice. As these mice respond in the improving quality of life.3 Although ART can keep same manner to HIV as humans do, measures that HIV at bay in most patients, infection persists and prove effective in combating HIV in humanized the virus can quickly rebound if therapy is inter- mice can be readily applied to human trials in the rupted. This is due to the fact that HIV can lay dor- hope that one day a cure will be found. mant in the cells of patients undergoing therapy. The ability of HIV to remain hidden in a patient is referred to as latency, and this component of HIV References 1. Denton, P. W.; Garcia, J. V. AIDS Rev. 2011, 13, 135-148. replication is one of the least understood. 2. Interview with Dr. J. Victor Garcia-Martinez, Ph.D. Since ART is only effective at suppressing in- 2/8/2012. fected cells that are actively producing virus, a sig- 3. Denton, P.; Olesen, R.; Choudhary, S. K.; Arachin, N. M.; nificant portion of HIV-infected T cells are able to Wahl, A.; Swanson, M. D.; Chateau, M.; Nochi, T.; Krisko, J. survive.3 This makes it impossible for the immune F.; Spagnuolo, R.; et al. J. Virol. 2012, 86, 630-634.

Spinal Muscular Atrophy: The Search for a Cure Shamra Byrne, Staff Writer

pinal muscular atrophy (SMA) is an incurable neuromuscular disease that is the leading genetic cause of early childhood mortality.1 Damaging the nerve cells responsible for muscle contraction in the spinal cord, SMA eventually leaves infants and toddlers unable to perform basic activities such as crawling, walking and swallowing (Figure 1). A number of therapeutic treatments exist for the disease, but as of yet, none have proven entirely effective. By improving our understanding of the functions of the gene products associated with the disease, Dr. Greg Matera and his laboratory at UNC-Chapel Hill hope to discover a cure. SMA is caused by a mutation in the survival motor neuron 1 (SMN1) gene that results in a deficiency of functional SMN, a protein critical for the health and survival of motor neurons.2 In humans, there are two nearly identical copies of this gene, SMN1 and SMN2. SMN1, the good twin, produces an abundance of the functional SMN protein; SMN2, the evil twin, does not.3 This is due to a simple silent mutation that does not even change the protein’s amino acid sequence. H owe ve r, because human SMN genes are differentially spliced, this seemingly insignificant Figure 1. A spinal muscular atrophy patient in his wheelchair. Image by easys- m u t a t i o n tand, [CC-BY-NC-ND 2.0]. causes a ma-

jor defect in RNA splicing, the process by which junk genetic material is removed and genetic material that contains functional genes is joined. This results in the loss of approximately fifteen amino acids essential for Dr. Greg Matera the production of a functional 4 SMN protein (Figure 2). Thus, when enough functional SMN protein cannot be produced due to an absence of the good SMN1 gene, the motor neurons will atrophy and eventually die. However, whoever said that two wrongs don’t make a right would be, well, wrong in this case. The SMN2 gene does have the ability to produce a small amount of functional SMN protein. An individual who has multiple copies of the SMN2 gene can often produce enough SMN protein to keep the motor neurons healthy and productive (Figure 3). The most severe cases of SMA occur when an individual has only one or two copies of the SMN2 gene. Individuals with three or more copies generally manifest less severe forms of the disease.2

Whoever said that two wrongs don’t make a right would be, well, wrong in this case. The SMN2 gene does have the ability to produce a small amount of functional SMN protein. Dr. Matera believes that the SMN protein is so important because of its part in the assembly of small nuclear ribonucleoproteins (snRNPs). Because snRNPs play a critical role in the processing of every protein in the body, it is essential that they are assembled correctly. “By studying how snRNPs are assembled and transported to their

Carolina Scientific Additionally, Dr. Matera is performing complementation studies with assorted transgenes in order to figure out whether or not the SMN protein has another role outside of maintaining the snRNPs that are required for life. A complementation experiment crosses one mutant with another mutant in an effort to see whether or not the two mutations can function together. If the mutations when crossed result in the recovery of the wild-type phenotype, it is assumed that both of the mutations occur in the Figure 2. At the protein level, the mutation responsible for the SMN2 same gene. In rare cases, two different gene is silent. However, due to differential splicing, it causes the loss of an entire fifteen amino acids from the tail-end of the manufactured mutations in the same gene will compleprotein, making it ineffective for the health and survival of motor neument each other. By making a series of rons. Image courtesy of Dr. Greg Matera. mutants with different point mutations in the SMN genes, Matera and his team sites of action inside the cell,” explains Dr. Matera, can cross each mutant with the others and fig“we hope not only to uncover basic mechanisms ure out if mutations complement each other inof cellular function but also to understand how Many researchers study the defects in this process might contribute to human 3 function of snRNPs in splicing, diseases like spinal muscular atrophy.” Many researchers study the function of snbut very few of them actually RNPs in splicing, but very few of them actually study how snRNPs are made in study how snRNPs are made in the first place. This the first place. This is the puris the purpose of Dr. Matera’s research. He says pose of Dr. Matera’s research. that these studies help his group to answer the question, “What are the consequences to the cell or organism when [this process] goes bad?”3 tragenically. “If they do [complement],” says Dr. Matera, “that suggests that there’s two or three different functions for that gene.”3 Such a discovery would then allow his team to figure out which regions of the protein interact with other proteins and cofactors within the cell, thereby facilitating the search for a cure. With ongoing research, the Dr. Matera laboratory hopes to uncover additional functions of the SMN protein. If they are successful, their research might eventually lead them to the underlying cause for the debilitating disease of spinal muscular atrophy. References Figure 3. Severity of SMA is inversely proportional to the concentration of SMN protein. Spontaneous abortion occurs in embryos below 10 percent of normal protein levels. SMA expression occurs between 10 percent and approximately 30 percent of normal protein levels. SMA is not observed in individuals above this range. Image courtesy of Dr. Greg Matera.

1. Eng, L.; Singh, D. About SMA. http://www.smafoundation.org/about-sma/ (accessed Feb 2, 2012). 2. Families of SMA. http://www.fsma.org/FSMACommunity/understandingsma/Prognosis/ (accessed Feb 2, 2012). 3. Rajendra, T. K.; Gonsalvez, G.; Walker, M.; Shpargel, K.; Salz, H.; Matera, A. G. J. Cell Biol. 2007, 176, 831-841. 4. Interview with Greg Matera, Ph.D. 01/31/2012.

Catching up with

Alexandru Bacanu By Garrick Talmage, Editor-in-Chief

I recently had the pleasure of interviewing Alexandru Bacanu, who is double-majoring in physics and mathematics with a minor in chemistry. Alexandru was recently awarded the prestigious Goldwater Scholarship, a testament to his potential to become an outstanding scientific investigator. His research in polymer physics exemplifies the creative and thought-provoking research that occurs at UNC-Chapel Hill.

What drew you to study polymers? Ever since I took my first physics class in high school, I knew I wanted to pursue a career in physics, but biology also fascinated me, so I started reading about biophysics, and then I realized that almost everything studied in biology is a polymer: DNA, proteins, carbohydrates and many more. We’re made of polymers! That’s when I first became drawn to the study of polymer physics.

Please briefly describe your research project. I am studying the method through which a molecule’s topology affects the distribution of tension within its bonds. Altering the distribution of tension in the molecule’s bonds can greatly change its physical properties, potentially allowing it to behave as a sensor or as a catalyst. The specific molecular topology that I am studying is called a “pompom,” because it looks like two cheerleader’s pompoms connected together by a linear spacer. Analytical calculations predict the bond tension be selectively focused in the spacer, and I am working on a computational model to describe the molecule’s tension distribution to verify if the theoretical predictions are valid.

How did you come up with the research question? I came up with the focus of my research with the help of Dr. Michael Rubinstein, the professor with whom I work. Dr. Rubinstein has been very encouraging and has helped me to grasp what research actually entails. In addition, his vast experience and deep knowledge base have been extremely useful whenever problems in my research arise. I wanted to do a project that involved computational work. In addition, I also wanted a project dealing with bond tension. There were several topologies that the Rubinstein group was studying, and I chose the one that seemed most interesting to me, the pompom.

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What are your future career plans, and how has your research experience at UNCChapel Hill prepared you to succeed in the future? How will the Goldwater Scholarship help you to achieve your career goals? After graduating, I plan to go to graduate school and pursue a doctorate in physics. After that, I plan to pursue a career in academia, doing research in biophysics. My research experience at UNC has been one of the deciding factors driving me to pursue a career in research. Our incredible faculty, as well as the phenomenal diversity and strength of Carolina research, has shown me that in pursuing a career in science, I will be challenged to think creatively as well as analytically as new problems arise. However, my academic and research experiences at UNC have equipped me to meet these difficulties; of course, research is never easy, but that’s where the fun arises from! The Goldwater Scholarship will help me achieve my career goals by reminding me that though research can sometimes be frustrating, diligence and Figure 1. The “pompom.” Image courtesy hard work are rewarded. of Alexandru Bacanu.

The Goldwater Foundation seeks to award highly motivated students interested in careers in mathematics, the natural sciences or engineering. Students that are selected “display intellectual curiosity and intensity and possess potential for significant future contributions in their chosen field.”1 Sophomores and juniors with a minimum GPA of 3.60 are eligible to apply through UNC-Chapel Hill’s Office of Distinguished Scholarships. Information about applying for distinguished scholarships, including the Goldwater Scholarship, can be found at http://honorscarolina.unc.edu/currentstudents/resources/office-for-distinguished-scholarships/. An information session on all distinguished scholarships will be held on Monday, August 29, 2012 at 5:15 PM in the Student Union Theatre. Interested students should contact the Office of Distinguished Scholarships at ODS@unc.edu. References

1. The Goldwater Scholarship. http://honorscarolina.unc.edu/ current-students/resources/office-for-distinguished-scholarships/the-goldwater-scholarship/ (accessed Apr 4, 2012).

Life after Graduation Seniors share their plans for life after May 13th

Garrick Talmage, the

Sophie Liu, the copy editor,

editor-in-chief, will be attending the University Of Chicago Pritzker School Of Medicine in the fall after graduating with a bachelor of science in chemistry.

will enroll in the chemistry Ph.D. program at the Massachusetts Institute of Technology after completing a bachelor of science in chemistry.

Hema Chagarlamudi,

Dasha Gakh, the

a design editor, will graduate with a bachelor of science in biology and Romance languages.

physical sciences editor, will graduate with a bachelor of science in chemistry.

Bhavesh Patel, a staff

Shamra Byrne, a staff

writer, will be entering a biomedical post-baccalaureate program after graduating with a bachelor of arts with a double major in exercise and sports science and biology.

writer, is moving to Portland, Oregon to work in technical device sales for the Keyence Corporation. She will graduate with a bachelor of arts in biology.

Morgan Locklear, a staff

writer, will become a part-time graduate student at the UNCChapel Hill Gillings School of Global Public Health and will apply to medical school. She will graduate with a bachelor of arts in biology.

Dylan Campfield, a

staff writer, will be taking post-baccalaureate classes. He will graduate with a bachelor of science in biology.

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Work for Carolina Scientific! Are you interested in communicating science to a broad audience?

thought-provoking investigations?

Do you want to engage in

Does your

passion for the sciences extend into the world of research?

Do you want to combine your creative talents with your fascination with the sciences? Carolina Scientific is always looking for staff writers, designers, and bloggers! If you are interested, please contact carolina_scientific@unc.edu.

Find us on facebook facebook.com/CarolinaScientific Follow us on twitter @uncsci Check out our blog carolinascientific.web.unc.edu

“Science is the topography of ignorance.” - Oliver Wendell Holmes, Sr.

Image by Ildar Sagdejev, [CC-BY-SA-3.0].

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Spring 2012 | Volume 4 | Issue 2

Thanks to Stephen Farmer and Donald Hornstein for funding and support. This publication was funded at least in part by Student Fees which were appropriated and dispersed by the Student Government at UNC-Chapel Hill.