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SMU students share their research at SMU Research Day 2018

SMU Research Day 2018 featured posters and abstracts from 160 student entrants who have participated this academic year in faculty-led research, pursued student-led projects, or collaborated on team projects with graduate students and faculty scientists.

SMU strongly encourages undergraduate students to pursue research projects as an important component of their academic careers, while mentored or working alongside SMU graduate students and faculty.

Students attack challenging real-world problems, from understanding the world’s newest particle, the Higgs Boson, or preparing mosasaur fossil bones discovered in Angola, to hunting for new chemical compounds that can fight cancer using SMU’s high performance ManeFrame supercomputer.

A highlight for student researchers is SMU Research Day, organized and sponsored by the Office of Research and Graduate Studies and which was held this year on March 28-29 in the Hughes-Trigg Student Center.

The event gives students the opportunity to foster communication between students in different disciplines, present their work in a professional setting, and share the outstanding research conducted at SMU.

Find out the winners of the poster session from the SMU Office of Graduate Studies.

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Solving the dark energy mystery: A new sky survey assignment for a 45-year-old telescope

SMU and other members of a scientific consortium prepare for installation of the Dark Energy Spectroscopic Instrument to survey the night sky from a mile-high mountain peak in Arizona

As part of a large scientific consortium studying dark energy, SMU physicists are on course to help create the largest 3-D map of the universe ever made.

The map will emerge from data gathered by the Dark Energy Spectroscopic Instrument (DESI) being installed on the Nicholas U. Mayall Telescope atop a mountain in Arizona.

The map could help solve the mystery of dark energy, which is driving the accelerating expansion of the universe.

DESI will capture about 10 times more data than a predecessor survey of space using an array of 5,000 swiveling robots. Each robot will be carefully choreographed to point a fiber-optic cable at a preprogrammed sequence of deep-space objects, including millions of galaxies and quasars, which are galaxies that harbor massive, actively feeding black holes.

“DESI will provide the first precise measures of the expansion history of the universe covering approximately the last 10 billion years,” said SMU physicist Robert Kehoe, a professor in the SMU Department of Physics. “This is most of the 13 billion year age of the universe, and it encompasses a critical period in which the universe went from being matter-dominated to dark-energy dominated.”

The universe was expanding, but at a slowing pace, until a few billion years ago, Kehoe said.

“Then the expansion started accelerating,” he said. “The unknown ‘dark energy’ driving that acceleration is now dominating the universe. Seeing this transition clearly will provide a critical test of ideas of what this dark energy is, and how it may tie into theories of gravitation and other fundamental forces.”

The Mayall telescope was originally commissioned 45 years ago to survey the night sky and record observations on glass photographic plates. The telescope is tucked inside a 14-story, 500-ton dome atop a mile-high peak at the National Science Foundation’s Kitt Peak National Observatory – part of the National Optical Astronomy Observatory.

SMU researchers have conducted observing with the Mayall. Decommissioning of that telescope allows for building DESI in it’s place, as well as reusing some parts of the telescope and adding major new sytems. As part of DESI, SMU is involved in development of software for operation of the experiment, as well as for data simulation to aid data anlysis.

“We are also involved in studying the ways in which observational effects impact the cosmology measurements DESI is pursuing,” Kehoe said. SMU graduate students Govinda Dhungana and Ryan Staten also work on DESI. A new addition to the SMU DESI team, post-doctoral researcher Sarah Eftekharzadeh, is working on the SMU software and has studied the same kinds of galaxies
DESI will be measuring.

Now the dome is closing on the previous science chapters of the 4-meter Mayall Telescope so that it can prepare for its new role in creating the 3-D map.

The temporary closure sets in motion the largest overhaul in the telescope’s history and sets the stage for the installation of the Dark Energy Spectroscopic Instrument, which will begin a five-year observing run next year.

“This day marks an enormous milestone for us,” said DESI Director Michael Levi of the Department of Energy’s Lawrence Berkeley National Laboratory , which leads the project’s international collaboration. “Now we remove the old equipment and start the yearlong process of putting the new stuff on.”

More than 465 researchers from about 71 institutions are participating in the DESI collaboration.

The entire top end of the telescope, which weighs as much as a school bus and houses the telescope’s secondary mirror and a large digital camera, will be removed and replaced with DESI instruments. A large crane will lift the telescope’s top end through the observing slit in its dome.

Besides providing new insights about the universe’s expansion and large-scale structure, DESI will also help to set limits on theories related to gravity and the formative stages of the universe, and could even provide new mass measurements for a variety of elusive yet abundant subatomic particles called neutrinos.

“One of the primary ways that we learn about the unseen universe is by its subtle effects on the clustering of galaxies,” said DESI collaboration co-spokesperson Daniel Eisenstein of Harvard University. “The new maps from DESI will provide an exquisite new level of sensitivity in our study of cosmology.”

Mayall’s sturdy construction is perfect platform for new 9-ton instrument
The Mayall Telescope has played an important role in many astronomical discoveries, including measurements supporting the discovery of dark energy and establishing the role of dark matter in the universe from measurements of galaxy rotation. Its observations have also been used in determining the scale and structure of the universe. Dark matter and dark energy together are believed to make up about 95 percent of all of the universe’s mass and energy.

It was one of the world’s largest optical telescopes at the time it was built, and because of its sturdy construction it is perfectly suited to carry the new 9-ton instrument.

“We started this project by surveying large telescopes to find one that had a suitable mirror and wouldn’t collapse under the weight of such a massive instrument,” said Berkeley Lab’s David Schlegel, a DESI project scientist.

Arjun Dey, the NOAO project scientist for DESI, explained, “The Mayall was precociously engineered like a battleship and designed with a wide field of view.”

The expansion of the telescope’s field-of-view will allow DESI to map out about one-third of the sky.

DESI will transform the speed of science with automated preprogrammed robots
Brenna Flaugher, a DESI project scientist who leads the astrophysics department at Fermi National Accelerator Laboratory, said DESI will transform the speed of science at the Mayall Telescope.

“The telescope was designed to carry a person at the top who aimed and steered it, but with DESI it’s all automated,” she said. “Instead of one at a time we can measure the velocities of 5,000 galaxies at a time – we will measure more than 30 million of them in our five-year survey.”

DESI will use an array of 5,000 swiveling robots, each carefully choreographed to point a fiber-optic cable at a preprogrammed sequence of deep-space objects, including millions of galaxies and quasars, which are galaxies that harbor massive, actively feeding black holes.

The fiber-optic cables will carry the light from these objects to 10 spectrographs, which are tools that will measure the properties of this light and help to pinpoint the objects’ distance and the rate at which they are moving away from us. DESI’s observations will provide a deep look into the early universe, up to about 11 billion years ago.

DESI will capture about 10 times more data than a predecessor survey
The cylindrical, fiber-toting robots, which will be embedded in a rounded metal unit called a focal plate, will reposition to capture a new exposure of the sky roughly every 20 minutes. The focal plane assembly, which is now being assembled at Berkeley Lab, is expected to be completed and delivered to Kitt Peak this year.

DESI will scan one-third of the sky and will capture about 10 times more data than a predecessor survey, the Baryon Oscillation Spectroscopic Survey (BOSS). That project relied on a manually rotated sequence of metal plates – with fibers plugged by hand into pre-drilled holes – to target objects.

All of DESI’s six lenses, each about a meter in diameter, are complete. They will be carefully stacked and aligned in a steel support structure and will ultimately ride with the focal plane atop the telescope.

Each of these lenses took shape from large blocks of glass. They have criss-crossed the globe to receive various treatments, including grinding, polishing, and coatings. It took about 3.5 years to produce each of the lenses, which now reside at University College London in the U.K. and will be shipped to the DESI site this spring.

Precise measurements of millions of galaxies will reveal effects of dark energy
The Mayall Telescope has most recently been enlisted in a DESI-supporting sky survey known as the Mayall z-Band Legacy Survey, which is one of four sky surveys that DESI will use to preselect its targeted sky objects. SMU astrophysicists carried out observing duties on that survey, which wrapped up just days ago on Feb. 11, to support the coming DESI scientific results.

Data from these surveys are analyzed at Berkeley Lab’s National Energy Research Scientific Computing Center, a DOE Office of Science User Facility. Data from these surveys have been released to the public at

“We can see about a billion galaxies in the survey images, which is quite a bit of fun to explore,” Schlegel said. “The DESI instrument will precisely measure millions of those galaxies to see the effects of dark energy.”

Levi noted that there is already a lot of computing work underway at the Berkeley computing center to prepare for the stream of data that will pour out of DESI once it starts up.

“This project is all about generating huge quantities of data,” Levi said. “The data will go directly from the telescope to the Berkeley computing center for processing. We will create hundreds of universes in these computers and see which universe best fits our data.”

Installation of DESI’s components is expected to begin soon and to wrap up in April 2019, with first science observations planned in September 2019.

“Installing DESI on the Mayall will put the telescope at the heart of the next decade of discoveries in cosmology,” said Risa Wechsler, DESI collaboration co-spokesperson and associate professor of physics and astrophysics at SLAC National Accelerator Laboratory and Stanford University. “The amazing 3-D map it will measure may solve some of the biggest outstanding questions in cosmology, or surprise us and bring up new ones.” — Berkeley Lab and SMU

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A Total Eclipse of the First Day of School

Dedman College, SMU Physics Department host Great American Solar Eclipse 2017 viewing

Thousands of students, faculty and townspeople showed up to campus Monday, Aug. 21 to observe the Great American Solar Eclipse at a viewing hosted by Dedman College of Humanities and Sciences and the SMU Department of Physics.

The festive event coincided with the kick-off of SMU’s Fall Semester and included Solar Eclipse Cookies served while viewing the rare astronomical phenomenon.

The eclipse reached its peak at 1:09 p.m. in Dallas at more than 75% of totality.

“What a great first day of the semester and terrific event to bring everyone together with the help of Dedman College scientists,” said Dedman Dean Thomas DiPiero. “And the eclipse cookies weren’t bad, either.”

Physics faculty provided indirect methods for observing the eclipse, including a telescope with a viewing cone on the steps of historic Dallas Hall, a projection of the eclipse onto a screen into Dallas Hall, and a variety of homemade hand-held devices.

Outside on the steps of Dallas Hall, Associate Professor Stephen Sekula manned his home-built viewing tunnel attached to a telescope for people to indirectly view the eclipse.

“I was overwhelmed by the incredible response of the students, faculty and community,” Sekula said. “The people who flocked to Dallas Hall were energized and engaged. It moved me that they were so interested in — and, in some cases, had their perspective on the universe altered by — a partial eclipse of the sun by the moon.”

A team of Physics Department faculty assembled components to use a mirror to project the eclipse from a telescope on the steps of Dallas Hall into the rotunda onto a screen hanging from the second-floor balcony.

Adjunct Professor John Cotton built the mount for the mirror — with a spare, just in case — and Professor and Department Chairman Ryszard Stroynowski and Sekula arranged the tripod setup and tested the equipment.

Stroynowski also projected an illustration of the Earth, the moon and the sun onto the wall of the rotunda to help people visualize movement and location of those cosmic bodies during the solar eclipse.

Professor Fred Olness handed out cardboard projectors and showed people how to use them to indirectly view the eclipse.

“The turn-out was fantastic,” Olness said. “Many families with children participated, and we distributed cardboard with pinholes so they could project the eclipse onto the sidewalk. It was rewarding that they were enthused by the science.”

Stroynowski, Sekula and others at the viewing event were interviewed by CBS 11 TV journalist Robert Flagg.

Physics Professor Thomas Coan and Guillermo Vasquez, SMU Linux and research computing support specialist, put together a sequence of photos they took during the day from Fondren Science Building.

“The experience of bringing faculty, students and even some out-of-campus community members together by sharing goggles, cameras, and now pictures of one of the great natural events, was extremely gratifying,” Vasquez said.

Sekula said the enthusiastic response from the public is driving plans to prepare for the next event of this kind.

“I’m really excited to share with SMU and Dallas in a total eclipse of the sun on April 8, 2024,” he said.

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NCI grant funds SMU research into cancer-causing viruses that hide from the immune system

Genes common to both the human T-cell leukemia virus and high-risk human papillomaviruses activate survival mechanisms in cancer cells. An SMU lab, with National Cancer Institute funding, is hunting ways to inhibit those genes to halt the development of cancer.

SMU virologist and cancer researcher Robert L. Harrod has been awarded a $436,500 grant from the National Cancer Institute to further his lab’s research into how certain viruses cause cancers in humans.

Under two previous NCI grants, Harrod’s lab discovered that the human T-cell leukemia virus type-1, HTLV-1, and high-risk subtype human papillomaviruses, HPVs, share a common mechanism that plays a key role in allowing cancers to develop.

Now the lab will search for the biological mechanism — a molecular target — to intervene to block establishment and progression of virus-induced cancers. The hope is to ultimately develop a chemotherapy drug to block the growth of those tumor cells in patients.

“The general theme of our lab is understanding the key molecular events involved in how the viruses allow cancer to develop,” said Harrod, an associate professor in SMU’s Department of Biological Sciences whose research focuses on understanding the molecular basis of viral initiation of cancer formation.

While HTLV-1 and HPV are unrelated transforming viruses and lead to very different types of cancers, they’ve evolved a similar mechanism to cooperate with genes that cause cancer in different cell types. The lab discovered that the two viruses tap a common protein that cooperates with cellular genes to help the viruses hide from the immune system.

That common protein, the p30 protein of HTLV-1, binds to a different protein in the cell, p53, which normally has the job of suppressing cancerous growth or tumor development. Instead, however, p30 manages to subvert p53’s tumor suppressor functions, which in turn activates pro-survival pathways for the virus.

From there, the virus can hide inside the infected cell for two to three decades while evading host immune-surveillance pathways. As the cell divides, the virus divides and replicates. Then ultimately the deregulation of gene expression by viral encoded products causes cancer to develop.

“They are essentially using a similar mechanism, p30, to deregulate those pathways from their normal tumor-suppressing function,” Harrod said.

Tumor suppression, DNA damage-repair pathways, begin to fail with age
About 15 percent to 20 percent of all cancers are virus related. Worldwide, about 10 million people are infected with HTLV-1 and, as with other viral-induced cancers, about 3 percent to 5 percent of those infected go on to develop malignant disease.

Cancer is often associated with the process of normal aging, because our tumor suppression and DNA damage-repair pathways begin to break down and fail, explained Harrod. Our pathways don’t as easily repair genetic mutations, which makes us more susceptible to cancers like adult T-cell leukemia and HPV-associated cervical cancers or head-and-neck carcinomas, he said.

The human T-cell leukemia virus is transmitted through blood and body fluid contact, usually infecting infants and children via breastfeeding from their mother. A tropical infectious disease, it’s endemic to Southeast Asia, primarily Japan, Taiwan, China and Malaysia, as well as certain regions in the Middle East, Northern Africa and islands of the Caribbean. In the United States, Hawaii and Florida have the highest incidence of adult T-cell leukemia. HTLV-1 is highly resistant to most modern anticancer therapies, including radiotherapy and bone marrow or matching donor stem cell transplants. The life expectancy of patients with acute or lymphoma-stage disease is about six months to two years after diagnosis.

In the case of HPV, certain high-risk sub-types aren’t inhibited by today’s available HPV vaccines. It’s considered the high-risk HPVs are sexually transmitted through direct contact with the tissues of the virus-producing papillomas or warts. High-risk HPVs can also cause cervical cancers and head and neck carcinomas, many of which are associated with poor clinical outcomes and have high mortality rates.

How do viruses cause cancer?
For both HTLV-1 and HPV, the virus itself does not cause cancer to develop.

“It’s cooperating with oncogenes — cellular genes that become deregulated and have the potential to cause cancer,” Harrod said. “The role of these viruses, it seems, is to induce the proliferation of the cell affected with cancer. We’re trying to understand some of the molecular events that are associated with these cancers. ”

The lab’s three-year NCI grant runs through 2019. Harrod’s two previous grants awarded by the National Institutes of Health were also three-year-grants, for $435,000 and $162,000. Each one has targeted HTLV-1 and the p30 protein.

The lab’s first NCI grant came after the researchers provided the first demonstration that p30 could cooperate with cellular oncogenes, which have the potential to cause cancer, to cause deregulated cell growth leading to normal cells transforming into cancer cells. That original discovery was reported in 2005 in the article “A human T-cell lymphotropic virus type 1 enhancer of Myc transforming potential stabilizes Myc-TIP60 transcriptional interactions,” in the high-profile journal Molecular and Cellular Biology.

“We find that the p30 protein is involved in maintaining the latency of these viruses. These viruses have to persist in the body for 20 to 40 years before a person develops disease. To do that they have to hide from the immune response,” Harrod explained. “So p30 plays a role in silencing the viral genome so that the affected cells can hide, but at the same time it induces replication of the affected cells. So when the cell divides, the virus divides. We call that pro-viral replication.”

The term “latency maintenance factor” in reference to p30 originated with Harrod’s lab and has gained traction in the HTLV-1 field.

Under the lab’s second NCI grant, the researchers figured out how to block pro-survival pathways to kill tumor cells.

In the current grant proposal, Harrod’s lab demonstrated that by inhibiting specific downstream targets of p53 — essentially blocking pathways regulated by the p53 protein — they could cause infected tumor cells to collapse on themselves and undergo cell death.

“We do that independent of chemotherapy,” Harrod said. “So that was a big find for us.”

Goal is to eliminate cancer cells by inhibiting pathway
Each grant project builds upon the one before it, and the third grant extends the work, to now include high-risk HPVs.

“Now that we’ve shown we can block one or two of these factors to cause cell death, we’re starting to get an eye really on how we can inhibit these cancer cells and what potentially down the road may lead to a therapeutic,” Harrod said. “That’s the ultimate goal.”

One of the biggest challenges will be to inhibit the pathways in the tumor cells without targeting normal cells, he said. The lab’s recent findings indicate the researchers may soon be within reach of identifying a new strategy to eliminate cancer cells by inhibiting pathways key to their survival.

Harrod’s lab collaborates on the research with: Lawrence Banks, Tumor Virology Group Leader, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy; Brenda Hernandez, Associate Director, Hawaii Tumor Registry, University of Hawaii Cancer Center, Honolulu; and Patrick Green, Director, Center for Retrovirus Research, The Ohio State University. — Margaret Allen, SMU

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SMU biochemists, students probe membrane proteins that thwart cancer chemotherapies

“Recurring cancers have ‘learned’ how to evade chemotherapy by pumping it out of the cancer cells so that only sub-therapeutic concentrations remain in the cell, making the drug useless.” — SMU biochemist Pia Vogel

The SMU undergraduate students and Dallas-area high school students get hands-on experience working on cancer research in the combined SMU Department of Biological Sciences laboratories of Wise and Vogel.

The researchers and students are working to find ways to treat cancer patients whose cancer has either returned after initial chemotherapy or was initially hard to treat using chemotherapeutics. The research is funded in part by the National Institutes of Health.

SMU Cancer Research

Students recently in the lab included Victoria Bennet, Hockaday School, and Shaffin Siddiqui and Robert Luo, both from Highland Park High School. SMU undergraduates included Hamilton Scholar Alexis Sunshine, Clinton Osifo, Stefanie Lohse, Brianna Ramirez, Henry Thornton, Shirely Liu, Justin Musser, Jake Oien and Michael Fowler. Also currently working in the lab are M.S. student and Hamilton Scholar Collette Marchesseau (2016 SMU graduate), and Ph.D. students Amila Nanayakkara, Mike Chen, Courtney Follit, Maisa Oliveira and James McCormick.

“Often, recurring cancers have ‘learned’ how to evade chemotherapy by pumping the therapeutic out of the cancer cells so that only sub-therapeutic concentrations remain in the cell, making the drug useless,” said Vogel, a professor and director of the SMU interdisciplinary research institute, the Center for Drug Discovery, Design and Delivery.

The pumps that do the work are proteins that span the cell membranes and use the biological fuel ATP to actively pump chemotherapeutics and other toxins out of the cells.

“We like to compare these proteins to biological sump pumps,” said Wise, associate professor.

Wise and Vogel use a combination of computational, biochemical and human cell-based techniques to find new drug-like compounds that inhibit the action of the pumps. If successful, the novel drugs — or derivatives of them — will be given to patients with therapy-resistant cancer together with the chemotherapeutic.

“Since our novel compounds block the pumps, the chemotherapeutic will remain in the cell and kill the cancer that had not been treatable previously,” Vogel said.

The researchers have discovered drug-like compounds that can be modified and developed into medicines that target the protein, called P-glycoprotein.

The SMU researchers discovered the compounds after virtually screening more than 10 million small drug-like compounds made publically available in digital form from the pharmacology database Zinc at the University of California, San Francisco.

Using SMU’s Maneframe high performance computer, Wise ran the compounds through a computer-generated model of the protein. The virtual model, designed and built by Wise, is the first computational microscope of its kind to simulate the actual behavior of P-glycoprotein in the human body, including interactions with drug-like compounds while taking on different shapes. The promising compounds were then tested in the lab.

“We have been quite successful and already have identified close to 20 novel compounds that block the pumps in our cell-based assays,” said Wise. “In these experiments we culture therapy-resistant prostate or ovarian or colon cancer cells in the lab and then show that we can kill these cancer cells using normal amounts of commonly available therapeutics in the presence of our novel compounds — even though in the absence of our novel compounds, the cancer cells would not be treatable.”

A pharmaceutical hit compound, like those discovered by Vogel and her co-authors, is a compound that is a promising candidate for chemical modification so it can eventually be delivered to patients as a therapeutic drug. In the case reported here, the compounds were commercially available for testing. The timeline from drug discovery to development to clinical trials and approval can take a decade or more.

SMU undergraduates and high school students experience world-class research
SMU undergraduate and high school students have been involved in different aspects of the research. Typically the beginning students work together with graduate or advanced undergraduate students to learn techniques used in the lab.

Some perform small research projects. Others have simply learned state-of-the-art techniques and “how science works” in the context of critical human health problems.

“High school student Robert Luo was interested in the computational side of our work, so he’s worked with senior SMU Ph.D. candidate James McCormick on trying to evaluate how strongly one of the therapy-sensitizing compounds we found potentially interacts with the pump protein at different proposed binding sites,” said Wise. “It is actually a significant project and will help with our research.”

The opportunities available for students to learn how science works using high performance computing, biochemistry and cell biology can be valuable even for those who won’t necessarily become practicing scientists, said Wise, citing as an example a recent SMU graduate who previously worked in the lab.

Ketetha Olengue (SMU ’15) is a good example,” he said. “She is now in her second year at the Keck School of Medicine at the University of Southern California, where she is pursuing her M.D. degree in a novel program with USC Engineering.” — Margaret Allen, SMU