Status: Endangered

I designed this info graphic to accompany a story I wrote for a city government assignment in a reporting class at UT. The story focused on the city of Austin’s intent to hire environmental consultants to survey for the presence of two endangered birds, the golden-cheeked warbler and the black-capped vireo, on land owned by the city. I designed the graphic using http://www.easel.ly to compare to the two bird species being surveyed. Click on the image to see an enlarged version.

Korzekwa Story #4 Infographic

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The Eyes Of Da’Marcus Baymon

I produced this audio slideshow in March 2012 for the College of Natural Sciences Office of Communications. I conducted the interview, edited the audio using Audacity, and chose and arranged the photos in SoundSlides. Alex Wang, the office’s photo intern, took the photos. During the interview Da’Marcus mentioned he could sing and in a burst of inspiration I asked him to sing the UT school song, “The Eyes of Texas,” which open and closed the piece nicely. The video was selected to be featured on the main UT webpage. It can be found at the following links: http://www.utexas.edu/know/2012/05/14/science_song_baymon/
http://cns.utexas.edu/news/8231

Sports allow writer to embrace sexuality and travel the world

I wrote this profile as the final longform story in my Reporting Sports class in 2014. Chuck Culpepper is a gay American sports writer who left the United States in 2006 after finding out his Columbian husband could not stay in the country. His passion for sports helped him through the experience, and he has now found himself back in the States, still blown away that some professional athletes are backing marriage equality. 

He sat at the bar in the Halcyon coffee shop in downtown Austin, Texas, with two glasses of wine to calm his nerves. Red wine — possibly pinot noir, if he remembers correctly.

This self-labeled “exotic creature” was writing the piece that could define him, as well as his career. He was ready to come out to the world as a gay sports writer.

“I’d been ready to write that for, I don’t know, five years, six years, maybe 10,” said Chuck Culpepper, who currently covers international sports for the website SportsOnEarth.com.

He had been at the Fourth Street coffee shop for almost four hours without making a single keystroke on the piece. At 7 p.m. he moved to the bar and ordered wine.

“I do that a lot, where I don’t wanna get started but when I do it goes pretty fast,” he said nine months later via Skype from Macau, near Hong Kong. “It was a different kind of column too because I already had all of the material. It should have been one of the easier ones.”

He thought it should have been easier because he now had a vehicle for his message. That vehicle came in the form of a 225-pound, 6-foot-1-inch NFL linebacker named Brendon Ayanbadejo, who then played for the Baltimore Ravens.

Ayanbadejo uses his social capital as a professional athlete to advocate for marriage equality in the United States. Culpepper thanked Ayanbadejo for his support in the Ravens’ locker room eight days before the 2013 Super Bowl, and the encounter left such an impression that the exchange became the motif of Culpepper’s coming out column titled “The Gay Super Bowl,” which was published on Feb. 7.

His piece racked up 68 comments on the website, more than 2,000 Facebook likes on its first posting, and thousands of retweets. The vast majority of the comments were positive. One of the top comments is from a sports writer who wrote how Culpepper had affected him personally.

“Chuck, never got to say it when I was in Lexington, but you inspired me to come out when I was on the sports desk there,” the comment reads. “Thank you.”

However, the column was only the end result of a long struggle for Culpepper.

Discrimination forced him to leave the U.S in 2006. That year Culpepper and his Columbian husband Alfonso knew they couldn’t stay in New York. At that time the U.S. had no provision to allow a long-term partner to reside in the country. So, the pair applied for visas in the United Kingdom. Culpepper was accepted and Alfonso was legally allowed there to come along as family.

“I felt like I had been kicked out and had no nationality,” he said. “It was really painful and it would hit me sometimes. I’d be walking to the gym and suddenly go, ‘Whoa, I can’t believe this is my reality.’ ”

While in London, Culpepper wrote a book about an English soccer team and covered European sports on a contract with the Los Angeles Times.

His journey through sports led him on adventure after adventure through the pain and suffering.

“Those experiences really did take me out of my pained mindset,” he said. “I was always off in exciting places and writing about really unusual things. There was no question that it mightily helped me through the fear and abandonment.”

After four years of living in a “walk-in-closet sized” apartment in London, Culpepper moved to Abu Dhabi, the capital of the United Arab Emirates, in 2010.

“Of course I wasn’t going to [write a coming out column] in Abu Dhabi,” he said. “It wasn’t going to get past the censors who look at the paper every night there. Nor did I have any interest in doing it there, going to jail or something like that. I was asked to keep it under wraps.”

So he waited even longer.

Culpepper moved back to the states in August 2012. He had an interview in New York for his current job at Sports on Earth upon his return.

“I talked to my bosses some and one of them asked if I was going to be really proactive about [the fact that I’m gay],” he said. “He wasn’t scared but he just wanted to see if I was going to be writing about the issue a lot. I said, ‘Yeah, I will be mentioning it sometime.’ ”

He was now just waiting for his moment.

And that moment came when he stepped into the Ravens’ locker room eight days before the Super Bowl.

“So it all just sort of came together, surprisingly, at that moment,” said Culpepper, now 51.

In his column he goes into detail about the event. He had forgotten Ayanbadejo was on the team until he saw his locker. He started an interview with professional football questions, but right before the linebacker walked down the tunnel Culpepper said something because he knew he would regret it for a long time if he didn’t.

“You don’t know me,” Culpepper wrote in the column, relaying the conversation, “but you have done a lot for me. And I just want to tell you that I am so grateful. You are a good man.”

To which the linebacker replied, according to the column: “It’s the right thing to do, plain and simple.”

Culpepper had ridden to that game with Steve Buckley, a gay sports writer in Boston, who had written his coming out column in January 2011. Buckley talked with Culpepper about what a great experience his column had been.

“It was really happenstance that that was the friend I happened to be around at that time,” Culpepper said.

Back in Austin a few days later, Culpepper left Halcyon after finishing his column at 10 p.m. He was renting a room in a house from retired food editor Amy Culbertson and he got her help editing the piece until 3 a.m.

“To me it was a real honor and a gift to be involved in this somehow not only for a personal friend who I have loved and admired for many years but also because in a sense it is a little historic,” Culbertson said.

She remembered that the beginning was the hardest part, and the pair worked on it for almost two hours.

“We kept trying and trying and eventually we got it to where it needed to be through a collaborative process,” she said. “I have edited some important work but this was probably the most important column I have ever gotten to be a part of because of Chuck personally and because of what it symbolized.”

Culpepper recalled being surprised he fell asleep from about 4 a.m. to 10:30 a.m. He woke up to emails from his boss in New York saying the piece was going up in 15 minutes, a warning he didn’t usually give.

“I remember walking around the house in those 15 minutes and thinking, ‘Well, you did it now,’ ” Culpepper said. “There’s a little bit of stress at that point no matter how ready you were. I don’t know why that is.”

The support rushed in almost immediately. Almost 100 sports writers who are his friends reached out to him in less than an hour.

“It just absolutely blew me away, even though I knew the reactions would be mostly positive,” he said.

He added that the only negative comments he got were from people saying they were tired of hearing about the gay community, which also left him stunned when he compared it to the country he left back in 2006.

“One thing that did amaze me was the tenor of the country I came back to after six years,” he said. “I had heard about it but living within it is a whole different thing. It had kind of been this big whoosh forward. I just couldn’t believe some of the things I was hearing.”

To this day Culpepper said there are still groups of people or friends who talk about it openly and genuinely with him and others that who don’t bring it up.

Through this entire journey from exile to gushing support a passion saw him through — a passion for sports that had developed by the age of 8. He said this passion is what allowed him to tell his story.

He watched everything: college basketball, the NFL, all of it. He would keep score, collecting huge notebooks of seasons of sports with newspaper clippings in them. He remembered having his dad keep score for him once while he went outside to do something, only to not like that a portion of the handwriting was not his.

When he was 14 a neighbor told someone at The Virginian-Pilot, the daily newspaper in Norfolk, Va., about Culpepper’s budding interests. He was soon writing updates on the little league games. He later wrote for his college newspaper at the University of Virginia.

“I think it’s the drama,” he said. “Sometimes I’ll go to YouTube and look at certain dramatic moments in sports and I’ll get chocked up still. It’s the unscripted drama and the way people react.”

Shane Whalley, of the Gender and Sexuality Center at the University of Texas at Austin, said that expectations of masculinity can be skewed in sports and cause gay men to have trouble coming out around sports. These perceptions can be even more intense in places like the locker room, Whalley said.

“Another reason you hear for why athletes don’t come out sooner is because they want to be known as Jenny the five-time Wimbledon winner, not Jenny the lesbian tennis player,” Whalley said.

When it comes to a sports writer like Culpepper, Whalley said many parallels can be drawn and sports writers can find themselves in similar situations, such as the locker room, and face the same issues with coming out as an athlete would.

“Stereotypes unfortunately persist and some people think anyone who is supposed to be an expert on sports isn’t as credible if they’re gay,” Whalley said.

Since the publication of his coming out column, Culpepper has written about the issue several more times and still travels the world covering sports, although he technically resides in Austin.

“This job has taken me to Mumbi, India. I had a dateline in the Philippines, and I had South Africa,” he said. “In late August they sent me around the world in 14 days to follow this sailboat race. I don’t know why they did this but it was incredible. In January I am supposed to go to Tanzania for a week and then in February to Russia for the Olympics, which should be interesting.”

While abroad, Culpepper’s position was as a reporter and not a columnist so there was no avenue for him to write this column. He did have opportunities before he left the U.S. in 2006 but thinks the outcome would have been different.

“I always think back to the year 2000 through late 2002,” he said. “That would have been a perfect time and I would have gotten plenty of support but it would have been more of a national thing. That was such a different time even then. I think it would have been discussed more along the lines of ‘well there’s something wrong with you.’ ”

He also said people each have their own time when they feel ready to tell the world their story.

“I don’t think my mind was ready back then,” he said. “We all develop at different paces and I think my mind wasn’t congealed enough, wasn’t ready enough, or sturdy enough at that time.”

Culpepper said he never feared that coming out would define him and his career. In fact, he would have welcomed it.

“I didn’t worry about that,” he said. “I wouldn’t have minded being recognized that way. I would think of it as something good. The only regret I have is that I didn’t do it 10 years sooner.”

You probably ate fungus today

The following clip is a research feature about endophytes, the fungi that live inside plant tissues, that I wrote for the College of Natural Sciences Office of Communications. It can also be found here: http://cns.utexas.edu/news/you-probably-ate-fungus-today

That salad you had for lunch. Yeah, it had fungi in it.

That celery stick you barely nibbled that came with your basket of wings last night. It had fungi in it too.

And it’s not just the plants you eat; the grass you walk on, the trees you walk under, and the flowers you admire all contain fungi. Actually, every plant tissue ever documented has fungi living inside it. They are called endophytes.

“Essentially most of us think of a plant as just a plant, but these plants are crawling with fungus,” said Christine Hawkes, associate professor of integrative biology in the College of Natural Sciences. “Every leaf, every stem, every root is full of fungus.”

Fungi are ubiquitous in plant tissues but every plant doesn’t contain the same species and most plants usually contain more than one species, potentially leading to vast amounts of undiscovered diversity, Hawkes added.

Endophytes are opening up an entire new frontier in the already swiftly evolving field of microbial ecology, the study of the distribution and interactions of microbes.

Scientists want to understand how the fungi hurt or help their host plant. Inside a plant these fungi can do two things: just hang out, a process called commensalism, or give the plant a variety of benefits in exchange for something, called mutualism.

The plants likely provide spare sugar to the fungi, while the documented benefits to the plant include improved tolerance to stressful conditions such as drought, heat, or salinity, as well as production of chemicals that act as protection against being eaten by herbivores, Hawkes said. While scientists understand some of these benefits, the full spectrum has not been realized and they are far from knowing how the fungi actually confer them to the plant. Teasing apart these benefits and mechanisms is the heart of the research taking place in the Hawkes lab.

While the group is interested in all of these interactions, they have been primarily focusing on drought tolerance. Water is a primary controller of plant productivity, and drought strongly limits production in both agricultural and ranching systems. While Texans may be accustomed to droughts, these conditions are expected to worsen in the future, she said. Fungal endophytes could provide a novel strategy for drought management, which is one goal in the Hawkes lab.

To study the endophytes, the researchers took advantage of a local steep rainfall gradient across the Edwards Plateau, where annual rainfall ranges from about 36 inches per year near Austin to roughly 16 inches by Del Rio. The Edwards Plateau is a region in west-central Texas that is essentially outlined by San Angelo, Austin, San Antonio and Del Rio, with the Hill Country making up its eastern portion.

The gradient allows them to compare fungi from plants that have historically received larger amounts of yearly precipitation to fungi from plants that experience more drought conditions year-round. In addition, by sampling the gradient across multiple years, it is possible to compare how these fungi respond to current conditions vs. historical rainfall.

“I grew up on the East Coast and lived in California,” Hawkes said. “When I moved here, I was thrilled to discover that I was living in one of the best precipitation gradients in the country, and that we were able to access research sites across the gradient through the Texas Parks and Wildlife Department and the Texas EcoLab program.”

Hawkes and her team survey 15-20 sites along the Plateau and collect plant and soil samples each year. They then isolate the fungi growing inside those plant samples. Once isolated, they can study the effects of the fungus on plants in the greenhouse.

Graduate students Hannah Giauque and Elise Worche have isolated and identified about 100 fungi from the Edwards Plateau so far. Giauque studies the effects of the endophytic fungi on drought resistance of switchgrass, a grass that is native to the U.S. prairies, and has shown large potential for use as a biofuel.

She got some surprising results, Hawkes said. They found almost an order of magnitude difference among about 30 endophytes in their effects on plant transpiration efficiency, which is how big a plant can get for the amount of water it uses.

“Essentially that variation is so huge that it suggests the fungus inside the plant matters a lot for how that plant can respond to its environment,” she said. “Which is something we don’t usually think about.”

However, they found that where the fungus came from didn’t necessarily reflect its function. While there were different species across the gradient, the location did not always reflect the ability of a fungus to confer drought tolerance, which was puzzling. A fungus from the dry end of the gradient isn’t necessarily a better mutualist for helping the plant resist drought when compared to one from the wetter side, like one would predict, and they are continuing to research why, Hawkes said. Rainfall is not the only important factor for a plant: some fungi may function as mutualists for the plant in ways that are not related to drought.

Another level of experimentation the researchers are working on is taking place at the Lady Bird Johnson Wildflower Center. There they are using a controlled plot to manipulate rainfall conditions. These rainfall conditions range from extreme drought to historical average to extreme wet, allowing the researchers to test how plants and fungi will respond at a single location to a range of climatic conditions.

Fungi can’t get up and walk around, so limitation in their dispersal may prevent rapid responses to a change in climate. In support of this, endophytic fungal communities across the 400-kilometer Plateau gradient have been stable during the three years the Hawkes lab has been sampling, even with annual changes in drought conditions. By planting grasses across a smaller area but still maintaining a precipitation gradient they are trying to tease apart how the different species end up where they do, and specifically predict how long it would take a new community to assemble in the face of climate change.

Worchel said the fungi don’t actually occur in isolation in nature and numerous species can be found inside one plant — even in just one two-inch leaf section — so the earlier experiments with one fungus in one plant aren’t necessarily representative of how they function in the natural environment. She is trying to learn how the fungi interact with each other but also with the plant when more than one fungus is present.

“I’m trying to figure out what the outcome is if you colonize a plant with both a mutualistic fungus and one that doesn’t have a positive effect,” she said. “Do you end up with a positive effect or does the commensal neutralize any positives? It can get complicated really quickly.”

Hawkes said that using the gradient, the field experiment, and greenhouse experiments provides different approaches to testing mechanisms with different levels of control and that together they create a very cohesive whole.

“The work that we’re doing eventually will help us to determine the potential for the endophytes to play a role in management of these grasses, particularly under drought,” she said. “There’s no final answer yet, but these preliminary results and ongoing experiments are very promising.”

Hawkes and her students are really at the forefront of this field.

“We aren’t building off of an extensive body of science for this,” Hawkes said. “It really is a new frontier. I realize that I could work on these few lines of research for the rest of my life and probably not have an answer. I think it’s both the challenge and what makes it exciting.”

Technological advances will only speed the process that could one day lead to plants that can better withstand climate change and other stresses, she added. At the end of the day, though, the entire lab agrees that the fact that these fungi are all around us is simply fascinating.

When giving talks about her research, especially the time she presented it over a dinner, Hawkes likes to remind everyone that, when they eat their leafy greens and other vegetables, they are also getting a healthy dose of fungus.

Q&A with “They Blinded Me with Science” crew

This Q&A is with the group of DJ’s that host the KVRX science radio show called “They Blinded Me with Science.” 

If you are looking for a local spin on science, tune to KVRX every Monday at 8:30 p.m. to catch “They Blinded Me with Science,” a radio show produced by graduate students in the College of Natural Sciences. And if you miss that, check out the podcast.

“It’s poetry in motion,” sings Thomas Dolby in the radio program’s namesake song, and indeed, grad students Nichole Bennett, Amanda Perofsky, Stavana Strutz and Michael Gully-Santiago bring the poetry of science to listeners’ ears weekly, covering research from UT Austin and around the world.

We sat down with the crew to ask how they came to be a part of the show and what role they think it plays in science.

Why do you think a show like this is important?

Amanda: I think it helps people see scientists as more approachable. There is this stigma that scientists are very pretentious, but we’re all just normal people who happen to be scientists, and I think the way we have discussions on the show helps people understand that.

Gully: From the listener point of view, they now have access to what’s going on in UT science. I think that’s really awesome. There are other outlets, but at least for now the radio and the podcasts I’ve been pushing are an easy way to get a digestible automatically downloadable format. The podcasts provide some real tangible thing that lasts beyond the fleeting airing of the show.

Do you think it brings anything to the communication of science?

Stavana: I feel like entertainment media is dominated by a lot of junk information, and so I feel what we present is real solid information. It’s facts in a fun-to-listen-to sense. And you know in the United States in particular science is sort of constantly being challenged, and so in a state like Texas I think it’s important to promote science.

Nichole: And on the flip side of that I sometimes feel like the radio show itself helps train our guests to be able to talk to the public. If you do some big research project and you get called by CNN you need to be able to kind of do that one line thing and get across your science but still keep the pubic engaged. I feel like we do a small part in trying to help with that.

Do you think the show makes you a better scientist?

Amanda: I feel like the show helps me be well rounded in terms of my scientific knowledge. If I were just left to my own devices I would probably just read infectious disease papers all the time and not necessarily branch out. Especially with having an astronomy person on the show I have learned a lot. I learned all about what the Higgs Boson is, for example.

Gully: We really have our pulse on what’s going on at UT because we’ve interviewed so many people now we sort of know what’s happening. Sometimes we have shows focused on national news where we just talk about current news instead of bringing on a guest. That also helps us keep our pulse on science that’s happening here at UT and around the world.

What are some of the coolest shows you all have done?

Nichole: We did a Valentine’s Day show on the science of kissing, and a Halloween show on the epidemiology of a zombie outbreak. So we pretended like it actually happened and how we would model it and how it was all kinds of hopeless, depending on the properties and transmissibility of the zombie outbreak. We also did a Sasquatch species distribution model. But the distribution of Sasquatch just happened to line up with the distribution of the black bear. So that’s a better explanation. We’ve done some fun shows.

Stavana: There is always something cool we learn on every show. There is always a crazy experience the guest scientist had. We have guests that come on that talk about all of their interesting adventures, like getting held up at gunpoint by poachers in India while looking at rare species of birds. Those are the kinds of things that get people excited about science.

How did you get started in the radio show?

Nichole: I joined my first year of grad school and am now the veteran member. I had always done college radio as a kind of hobby. Then someone came to me and said, “Oh, we have a science show and you should join it.” And honestly I wasn’t really comfortable at first having my music life and my science life interact. But actually it’s a really great way to learn how to talk about your research.

Gully: So I got involved originally as a guest in December of 2012. I then sort of just started coming on as a host the semester after that. It was just occasionally at first and now I’ve more or less been doing it pretty steadily this summer and fall. I was also the one that started the podcasts.

Amanda: When I was interviewing for grad school here I mentioned to someone in our department that I wanted to DJ at the radio station because I really enjoyed being a college radio DJ in undergrad. That’s when someone told me about the science show and said that I should meet Nichole. In college I had thought it would be cool to do a science talk show but I never had the initiative to start one up on my own. When I came here it was just something I could join right away. I’ve been doing it for two years now.

Stavana: I was a guest in September 2012. After that I became a regular guest, really. Then, Nichole told me, “you’re a good guest speaker and I’m leaving for five months to Japan so can you come on and fill my shoes?” I was very happy to do it. It’s a great opportunity. We are also really glad Gully is here so it’s not just biologists.

“They Blinded Me with Science” hosts Nichole Bennett, Amanda Perofsky and Stavana Strutz are graduate students in the Ecology, Evolution and Behavior program. Michael Gully-Santiago is a graduate student in Astronomy.

Senior blends jazz performance and neuroscience

The following is a Q&A with Mason Hankamer, a neuroscience and jazz performance major, which will be featured in our alumni magazine. Along with interviewing Mason and putting the piece together, I was the one who pitched the idea at an editorial meeting. I chatted with Mason for nearly an hour to get to the bottom of this interesting choice of majors. It is one of four Q&A’s going in the magazine; we are also featuring a graduate student, a professor and an alumna.     

Q&A: The Undergraduate

Name: Mason Hankamer
Year: Fourth
Majors: Neuroscience and Jazz Performance

Korzekwa: So what do you like about neuroscience?
Hankamer: There is so much that we don’t know about the brain. There is just so much to figure out and who knows what we can do with it once we know how it can be applied.

What is your history with the Longhorn Band?
I joined the Longhorn Band to march my freshman year and have been in it every year since. Although I’m a jazz bass major, I play the tuba in LHB, and have been a section leader for the past two years. It’s such a great organization with amazing people.

And how did you realize you wanted to add jazz performance as a major?
I’ve always really loved music. Doing neuroscience by itself just felt like there was an empty hole, but at the same time, if I were just to do music there would be this entire gap where my academic thinking was missing.

How do you think the two majors come together for you personally?
I have what’s called color synesthesia, where I see music in colors. Certain sounds and instruments have different colors. For example, a song could be deep purple with sharp streaks of orange. I like playing bass instruments because they produce a dark blue color to me. When I compose, it’s like I’m painting a picture. I don’t actually see them physically; it’s more the aura of the color, which is difficult to explain. What really links the two is that we studied the condition once in a neuroscience class. It was really neat to actually learn and understand why I experience this.

What are some ways you think music and the brain are connected?
I am always thinking about music. Just humming a song in my head during class makes me ask so many questions. How and why do songs get stuck in your head? How and why does this song make me feel this way? I think it’s amazing how music completely inundates our entire lives. Take a look at ACL [Austin City Limits Music Festival]. Walk across campus and see everyone with their headphones. It’s a weird force that controls a large portion of our lives whether we think about it or not. There has kind of been this cultural phenomenon created at the intersection of music and the brain.

Science Essentials

The following three short clips are the Science Essentials section in the first edition of the College of Natural Sciences’ alumni magazine. For these pieces the participating faculty had two options: they could write something up that I would edit or I could interview them and ghost write something for them to look over. All of them chose the interview option. Regardless of the approach, the short articles will appear in the magazine authored by the faculty member but the interview, tone, organization and editing are from me. I worked with the professors to narrow their focus and pull their thoughts together into an easy-to-understand narrative. 

Science Essentials: Exoplanets
By Bill Cochran, Astronomy

There was a time when we thought we were special, that our sun was the only star with planets. Now, we know better. When I started in this field, we were just barely predicting the presence of exoplanets — planets that orbit other stars — and now we have proven the existence of more than 1000. The count is climbing every day.

As we looked at the sun and wondered why we have planets here, we compared the sun to other stars and were a little disappointed. We realized the sun is not special. The sun is just like all of these millions of other stars out there. There’s absolutely nothing about our star that would lead to us to think there should be planets here and not elsewhere.

So when we started looking and finally figured out how to take the measurements and do the calculations correctly we figured out that all of those other stars out there also have nice planetary systems around them. Current estimations say that every star has at least one planet orbiting around it.

It sort of puts our role in the universe into perspective — we really aren’t that special. You know this is one of the last places where humans can do exploration. Hundreds of years ago people would jump in a ship and find new worlds and now I go up to my telescope to find new worlds.

Science Essentials: RNA
By Chris Sullivan, Molecular Biosciences

RNA has come a long way in just a few short years. Once the ugly stepchild of the nucleic acids, it was thought to be a boring and simple message decoder (Remember the Central Dogma?). RNA, a polymer composed of four different nucleotides connected by a sugar ribose backbone, took a backseat when researchers discovered DNA was the genetic material.

RNA does serve as the intermediate between DNA and proteins, decoding the DNA and then being translated by the ribosomes that make proteins, but that is only a sliver of its diverse set of functions.

The molecule has very interesting structural and enzymatic functions, making it similar to proteins. A large amount of what was once thought of as “junk DNA” is actually transcribed into RNA and used for a variety of functions. Given the vastness of these RNA and their potential to unravel numerous mysteries of biology, collectively the RNAs have been referred to as the “dark matter” of the genome.

Regulatory RNA, for example, seem to turn on or off certain genes. These small RNAs can be synthesized and used to silence any gene, and this has exploded into a multi-billion dollar industry known as RNA interference.

MicroRNA, another type, serve as dimmer switches during gene expression, and are involved in almost all aspects of development and disease. Despite this, we only understand the functions of a miniscule fraction of RNA, so clearly more fireworks await discovery.

The vast functions of RNA have even led scientists to theorize that life started in an “RNA World,” where RNA came first because it can perform so many processes and DNA evolved as the genetic material later.

Science Essentials: Scanning Tunneling Microscopy
By Lauren Webb, Chemistry

Our understanding of the structure of an atom hasn’t changed since the early 20th century, but the way we visualize them certainly has. Scanning tunneling microscopy (STM) is now the norm, and it is a critical tool we use to visualize atoms and molecules and understand their structure.

We have all learned how electrons occupy regions of space around atoms, called “orbitals.” However, it turns out these electrons sometimes move outside of their atomic orbitals. This happens in such a predictable manner that if you put two objects very close to each other they will begin to share electrons. In STM, we literally take an electrode and bring it very, very close to the surface of the material we’re studying. We get it so close that the materials begin to share electrons, which in turn creates a current. This current is what we can measure.

The properties and function of a material are determined by its structure. We used to not be able to see the individual atoms and molecules of these materials, but now that we can using STM, the mysteries behind many materials have been solved. That’s really what chemistry is all about right now — understanding how the properties of individual molecules combine and work together to create new properties in both artificial and biological materials.

Some, for example, have used the technique as a tool to pick up and drag individual atoms and molecules, literally organizing them. If we could do this on a large scale, it opens up all sorts of completely new fabrication and synthesis mechanisms.

Cracking the genetic code of brain tumors

The following clip is a research feature story published on the Texas Science website and also the main University of Texas at Austin webpage. It can be found at the following links:
http://web5.cns.utexas.edu/news/2012/09/glioblastoma-genetics-iyer/
http://www.utexas.edu/know/2012/09/28/brain-tumor-glioblastoma-genetic-code/

When patients are diagnosed with glioblastoma, one of the worst forms of brain cancer, their options are limited.

Even after surgically accessing the brain to remove as much of the tumor as possible and applying intense chemotherapy, the prognosis is poor. The average survival time is about 14 months.

Vishy Iyer, professor of biology, and Matt Cowperthwaite, research director of St. David's NeuroTexas Institute. Photo by Alex Wang.
Vishy Iyer, professor of biology, and Matt Cowperthwaite, research director of St. David’s NeuroTexas Institute. Photo by Alex Wang.

“There are really no good treatments,” said Vishy Iyer, a professor of molecular genetics and microbiology in the College of Natural Sciences at The University of Texas at Austin, who is trying to change that. “You can do surgery and chemotherapy, but glioblastoma is just bad to have.”

Symptoms can start as headaches and nausea. If ignored, the tumor continues to grow, putting pressure on other parts of the brain. Seizures appear. As the tumor’s size increases further, the pressure in the skull becomes life threatening as even far reaches of the brain are bruised against the skull. This begins the progressive deterioration of personality and memory.

Before surgery —  even before symptoms appear — a cancerous tumor starts as what can only be considered a freak accident: a mutation, a random change in a cell’s DNA that leads to uncontrolled cell division. Different mutations cause different cancers and even different molecular subtypes of cancers.

Using these mutations to classify subtypes could lead to better, more personalized treatments for glioblastoma. That’s what Iyer — in collaboration with Matt Cowperthwaite, director of research at the NeuroTexas Institute at St. David’s HealthCare — is hoping to be able to do.

Iyer and Cowperthwaite are taking advantage of two resources: the Austin Brain Tumor Repository started by Cowperthwaite and a technology known as next-generation, or “next-gen,” sequencing.

“Compare making an old-fashioned, smudged fingerprint with ink to making fingerprints with a high-resolution, digital scanner,” Iyer said. “The results we can now obtain, thanks to next-gen sequencing, can be very powerful and very exciting.”

DNA sequencing is the process by which scientists determine the order of the nucleotide bases — thymine, adenine, guanine, cytosine — in a piece of DNA. Next-generation sequencing, a concept first developed in 2004, provides a way to perform this task more quickly and less expensively.

Conventional sequencing processes can process DNA at approximately 100,000 bases per day with a cost of about 5 cents per base. Iyer’s group uses the next-generation sequencing techniques to sequence roughly 1 billion bases per day at about 0.00002 cents per base.

What this sequencing will allow them to do, said Cowperthwaite, is get a better insight into the individuality of tumors.

“You and I could both have the same type of tumor, in the sense that the clinical diagnosis may be glioblastoma, but yours may be different from mine,” he added. “And I feel as if this research will lead to a better understanding of what is driving those differences.”

The researchers believe that a source of these differences may be mutations in or around molecules known as transcription factors.

“Transcription factors are switches,” Cowperthwaite said. “Essentially they are like light switches; they turn genes on and off. They typically only control particular light switches. But, as the tumors accumulate mutations and change, they may learn how to turn on new lights, or they may lose the ability to turn on or off some lights they normally control.”

To identify these mutations Iyer is using a technique that can essentially identify and isolate what part of the DNA the transcription factors associate with. That DNA is then sequenced specifically in search of mutations.

“Our project is taking a unique approach by focusing on the cancer’s regulatory pathways and the DNA mutations that take place inside the tumor’s regulatory pathways instead of sequencing the entire genome of the cancer like many researchers are currently doing,” Iyer said.

The project uses a sort of double comparison. Iyer and Cowperthwaite have access to both tumor sample DNA and blood sample DNA for each patient. First, they compare these two samples to see what mutations are unique to each tumor.

Then, because Cowperthwaite has given Iyer access to many glioblastoma samples, they plan to compare the mutations against those in all of the other tumors using sophisticated computing software.

Cowperthwaite started the Austin Brain Tumor Repository in 2011. He and his team work closely with neurosurgeons and neuroncologists to learn of tumor operations taking place at the hospital.

“Normally, most of the tumor tissues that are removed during surgery are discarded as biowaste,” he said, adding that besides the initial purchase of a powerful freezer, the tumor bank has been relatively inexpensive to maintain. “When we learn of an operation, we go in and ask the patient if they would want to donate their tumor tissue to research. The vast majority says it’s an easy decision.”

Determining the patterns of different mutations in different tumors will allow the team to identify molecular subtypes of the cancer. The hope of the researchers is that this information can one day be used to develop personalized therapies for cancer.

“Instead of a treatment like chemotherapy that hits all dividing cells, we may be able to use drugs that target specific types of subtypes of tumors,” Iyer said. “Identifying different subtypes based on different interrupted regulatory pathways will allow for the use of specific drugs that interact with specific pathways.”

Although Iyer and Cowperthwaite are still trying to identify the molecular subtypes of glioblastoma and years of more research would be needed to produce these specific drugs, there are several possibilities for treatment if the dream is realized.

If the cancer is caught in an early stage, its growth could be halted by disrupting the specific pathways that keep it dividing and functioning. At later stages there is the possibility of removing a large part of the tumor and then stopping the growth of what remains. This could result in permanent remission.

“Cancer is moving out of this phase of just finding the changes that caused the tumor, which we were doing just five years ago,” Cowperthwaite said. “Inventories of mutations are interesting catalogs, but translating that into something that is actionable is becoming more prominent. That movement is what Vishy and I want to be a part of. Perhaps someday we will be able to run detailed genetic tests on a patient’s tumor and say, ‘Here’s a treatment plan that will cure your disease.’ ”