SJSU Students Use Bioinformatics to Study How Living Organisms React to Space Travel

International Space Station

SJSU bioinformatics students helped NASA scientists better understand how living organisms react to life on the International Space Station compared to Earth. Image courtesy of NASA.

How does space travel impact the human body? That’s a question scientists are still trying to answer. This summer, they got a little closer to the answer, thanks to some extra help from San José State University students.

A cohort of biology and computer science undergraduate students were the first to participate in San José State’s new bioinformatics internship program with NASA, developed by two SJSU College of Science faculty: Philip Heller, assistant professor of computer science, and Bree Grillo-Hill, assistant professor of biology.

Equipped with knowledge from their SJSU biology and computer science courses — plus training from a bioinformatics bootcamp — six students joined NASA’s GeneLab project. They helped analyze and interpret publicly available data that revealed the RNA of different organisms, including humans, plants, insects and mice, in order to compare how those organisms responded to life on the International Space Station compared to Earth. The internship began in June and ended in August.

“The goal was to gain insights into the biological processes that degrade astronauts’ health in microgravity and other stressful conditions,” explained Heller. “These insights will drive decisions about lowering astronaut health risks, so the implications for science are profound.”

For example, Evelyn Wong, ’21 Biology, analyzed data to help NASA researchers better understand how and if cancer could be a risk following space travel.

“Astronauts are exposed to radiation when traveling to space, which makes them likely candidates for developing cancer later in life,” she explained. “I studied samples that might be able to help identify that possibility for developing cancer in the future.”

Wong said she’s not a natural programmer, so the internship offered her an opportunity to gain new data processing skills while putting her biology knowledge to use. Her hard work paid off: After her internship wrapped up in August, Wong began working as a full-time research associate contracted by Blue Marble Space Institute of Science to work with NASA.

That’s the kind of success Heller was hoping his students would achieve when he developed the internship. Bioinformatics is an increasingly important field, he noted. San José State offers a minor in bioinformatics as well as a master’s degree.

Preserved tissue samples

Publicly available data gathered from preserved tissues such as those seen here, archived at the NASA Ames Research Center, were analyzed and interpreted with the help of SJSU bioinformatics students. Image credit: NASA/Dominic Hart

Grillo-Hill emphasized that the experience can give students an edge in job searches and graduate school applications.

“Many cutting-edge projects in biology research require generating, managing and analyzing large data sets,” she explained. “Our bioinformatics minor teaches students the tools to do this, and internships give them the opportunity to practice these skills on real data sets.”

With NASA’s Artemis program to land humans — the first woman and first person of color, specifically — on the moon in 2024, “the urgency is high” to better understand how humans respond to space travel, Heller emphasized.

He hoped to create a program that would allow both SJSU and NASA to reap the benefits. SJSU could supply a steady stream of talented students interested in bioinformatics, and the next generation of scientists could gain valuable first-hand interdisciplinary experience, he said.

While this isn’t the only opportunity SJSU students have to intern with NASA — the College of Engineering, for example, helps place aerospace engineering students into internships with the agency — it’s the first chance for SJSU students interested in bioinformatics.

To make sure students were ready to hit the ground running, Heller, in collaboration with NASA GeneLab and Universities Space Research Association, kicked off the program with a five-day intensive bootcamp that acquainted students with NASA’s processes and goals and provided a deeper understanding of the field.

Kevin Truong, ’22 Computer Science, found the experience of working in an interdisciplinary environment with NASA scientists eye-opening.

“Working in bioinformatics gave me the opportunity to explore different fields and to learn things I didn’t know — and that I’ll likely never understand. And that’s OK if there is someone else on your team who can explain it. Sometimes, I will be the one to explain things to someone else.

“It’s a fascinating field and can be challenging, but in the end you get to create greater things.”

Heller emphasized that “even if the interns don’t become NASA scientists, they will gain training and experience in techniques that are commonly used in biotech, so we believe their long-term career experiences will be greatly enriched.”

Aeowynn Coakley, ’21 Biology, already feels that her future as a research scientist has been influenced by the experience.

“Whatever I do next, I want to work with an interdisciplinary team. You can go so much further and understand so much more working together that way,” she said.

“Bioinformatics is a really important tool to make meaningful inferences about data being collected,” she continued. “We are in an era of big data, and there’s so much biological information out there and so many scientists working siloed as they delve into this data. Through bioinformatics, we can make really meaningful contributions to the field by introducing an interdisciplinary perspective.”

Learn more about San José State’s MS in Bioinformatics and minor in Bioinformatics.

Civil Engineering Student Andrea Coto Earns NSF Graduate Research Fellowship

SJSU student Andrea Coto presented work with SJSU AVP for Undergraduate Programs Thalia Anagnos at the Stanford Blume Center/SURI Affiliates/Alumni Meeting in fall 2018. Coto, '19 Civil Engineering, has received a National Science Foundation Graduate Research Fellowship to pursue a graduate degree at Stanford.

SJSU student Andrea Coto presented research with SJSU AVP for Undergraduate Education Thalia Anagnos at the Stanford Blume Center/SURI Affiliates/Alumni Meeting in fall 2018. Coto, ’19 Civil Engineering, has received a National Science Foundation Graduate Research Fellowship to pursue a graduate degree at Stanford.

By Abby McConnell, SJSU Office of Research

Despite her acceptance to graduate school at Stanford in the fall and an impressive undergraduate career, which boasts three associate degrees, internships with NASA and the Port of San Francisco, along with participation in the McNair Scholars Program, the Engineering Leadership Pathways Scholars Program (ELPS) and the Stanford Summer Undergraduate Research Programs (SURF), Andrea Coto is still a bit shocked that she was recently awarded a National Science Foundation Graduate Research Fellowship (GRFP). Securing a fellowship is intensely competitive: For the 2018 competition, NSF received over 12,000 applications and made 2,000 award offers.

Andrea Coto poses at a project at the Port of San Francisco in 2019.

Andrea Coto poses at a project at the Port of San Francisco in 2019.

The GRFP is the oldest graduate fellowship of its kind, and recognizes outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master’s and doctoral degrees. NSF Fellows often become knowledge experts who contribute significantly to research, teaching, and innovations in science and engineering.

In the more immediate future, the fellowship will fund three years of Coto’s graduate program. While still processing the news, she is already mapping out the possibilities. Her NSF proposal and anticipated graduate research will focus on one of her passions: sustainable design and construction as it relates to extreme environments, specifically outer space.

“Space exploration is really a giant lab, right?” she said. “I want to bring that research back to earth.”

When asked how she’s achieved so much in such a short time, she shrugged and smiled. “I apply to programs I’m interested in,” she said. “I figure they have to pick someone, so why not me?’”

From El Salvador to the Mission District

Several years ago, Coto herself might have doubted this kind of self-assuredness. If not for a handful of key mentors, she said, she wouldn’t have made it this far.

Coto was born in the Bay Area, but much of her young life was spent in El Salvador, the native county of both her parents. After their separation and divorce, Coto’s mother was left to raise Coto and her brother on her own.

“My mom is the most resilient and resourceful person I have ever met,” Coto said. “She even learned to bake so she could sell bread to pay our bills.”

Although Coto earned a technical degree in civil engineering in El Salvador, upon graduation, there were no job opportunities. Soon afterward, relatives in San Francisco invited her to come live with them. Coincidently, she had saved just enough money for a flight to the Bay Area. She was hesitant to leave her family and her boyfriend behind, but she knew it was the only way.

Her early days here were challenging, from trying to learn conversational English to working at a Dollar Store in the Mission for $6 an hour. Things shifted when she started taking non-credit ESL classes at City College of San Francisco, and her English language skills were buoyed by her work in retail, which included selling shoes at Macy’s.

Andrea Coto, '19 Civil Engineering, participated in NASA's Community College Aerospace Scholars program while earning an associate's degree.

Andrea Coto, ’19 Civil Engineering, participated in NASA’s Community College Aerospace Scholars program while earning an associate’s degree.

She eventually matriculated at the Ocean City College campus, where she met a key mentor, Dr. Edgar Torres. After a difficult semester juggling three jobs and failing Calculus II, she told Torres she was going to drop out.

“I told him I wasn’t smart enough to be an engineer,” she said. “He told me that wasn’t the problem, and that I should take the class again with a different professor. I did, and got a B+.”

Early mentors like Torres were invaluable to Coto, and she has consistently sought out female and Hispanic engineers, graduate students and professors as role models along the way.

“I don’t believe in the ‘you can’t see, you can’t be’ philosophy, but representation is incredibly important,” Coto said.

Finding a ‘Pathway’ at SJSU

Andrea Coto joined SJSU as a transfer student. Here she poses for a photo on Admitted Spartans Day after she accepted admissions to SJSU.

Andrea Coto joined SJSU as a transfer student. Here she poses for a photo on Admitted Spartans Day after she accepted admissions to SJSU.

Once at SJSU, she worked diligently to leverage the resources available to her. She also credits professors and administrators such as Dr. Laura Sullivan Green from the Department of Civil and Environmental Engineering, McNair Scholars Director Dr. Maria Elena Cruz, and Engineering Leadership Pathway Scholars program founder Dr. Thalia Anagnos, for guiding her and showing her what was possible.

Anagnos created the ELPS program in partnership with the NSF, and it has provided scholarships, mentoring, leadership and career development to more than 70 low-income, academically talented students at SJSU.

While they have all been exceptional, Anagnos said Coto stands out. “From her first weeks at SJSU, she sought opportunities to both better herself and give back,” she said. “Andrea is a natural leader in all areas of her life—academic, professional and personal—but she also brings a genuine optimism to her every interaction.”

Even when discussing the recent death of her father, that optimism is evident. Coto learned he had terminal cancer in the midst of applying to graduate schools and the NSF program. As she toured places like MIT and Stanford, she sent him photos and videos so that he could share in the experience. She also returned to El Salvador several times last fall to visit him.

“Being there with him before he died healed a lot of things,” she said.

Looking Toward the Future

Despite this loss, she continues to move forward. Her mother, brother and her boyfriend (who is now her husband) were able to join her in the U.S. in 2013, and she views her accomplishments as collective achievements. “All that really matters is that we are together,” she said.

As graduation nears, Coto is focused on yet another goal: outreach. She wants underrepresented students like herself to hear her story and see where they can go, and in the process, hopefully shift negative narratives around Latino immigrants.

“Storytelling is powerful. I believe it’s the way we change lives and perspectives, especially in light of the current administration,” she said. “I want to fight the misconceptions about El Salvadorians and other immigrants from my own ‘trench’ in this way, in order to increase knowledge and understanding.”

Stellar student researches stellar noise

SJSU physics student Stephanie Striegel is involved in research that could help scientists discover new exoplanets.

SJSU physics student Stephanie Striegel is involved in research that could help scientists discover new exoplanets.

Stephanie Striegel is set to graduate this spring with a bachelor’s in physics but she already has her sights set high — beyond this galaxy to be exact. Last summer, Striegel interned at the Carnegie Observatories in Pasadena with Dr. Johanna Teske, where they conducted research on mitigating stellar noise using high cadence radial velocity observations for the purpose of detecting small exoplanets. Exoplanets are planets that orbit a sun other than our sun, according to NASA. Scientists are particularly interested in identifying these bodies beyond our galaxy in their search to find a place that might be habitable.

Striegel’s summer internship was offered through the CAMPARE program, which recruits students from California State University and California community colleges to engage in research, with a goal of increasing underrepresented students in the sciences. She was awarded a $3,000 grant from Sigma Xi Grants-in-Aid of Research program to fund an observing run at Las Campanas Observatory in Chile to collect more data on her stellar noise project with Teske during the school year. According to Sigma Xi, 12 percent of the 810 applicants who applied were approved for funding, and of those approved, only 17 percent were undergraduate students.

While she completes the final courses of her undergraduate career, Striegel is also engaged in an internship at NASA’s Ames Research Center (ARC). She is working with Dr. Tom Greene on reducing laboratory data and performing detector characterization for infrared instruments to enable future studies of habitable exoplanets.

“The classes at SJSU have prepared me for my internships both at Carnegie Observatories and NASA ARC,” she said. “Our physics department has a focus on computational physics, which has been especially useful since a lot of astronomy research requires programming skills.”

Before beginning her internships, Striegel worked with Associate Professor Aaron Romanowsky’s student research team. His research group was focused on ultra-compact dwarf  (UCD) galaxies, which are brighter and more compact than typical dwarf galaxies. Her task included mining the Sloan Digital Sky Survey catalogue for possible candidates by analyzing the characteristics of confirmed UCDs and using SQL queries to do comparisons around galaxies in the local universe. Along with other scientists, Romanowsky’s team hopes to discover how UCDs were formed, specifically if they were part of larger galaxies.

“I’m very grateful for the Physics and Astronomy department at SJSU,” she said. “My peers and the faculty here have been nothing but supportive, and every internship or opportunity I’ve had, I owe to them.”

Cube Satellite Launches to International Space Station

By Sarah Kyo, Web Communications Specialist

TechEdSat, a NASA-sponsored cube satellite that SJSU aerospace engineering students have worked on, launched from Japan to the International Space Station.

NASA TV began its live-stream coverage on Friday, July 20, 6:15 p.m. PDT. Then 7:06 p.m. was the official launch of the Japanese transfer vehicle, which contains TechEdSat and four other cube satellites from international universities and organizations.

“Cubesats have been around, but this is the first ever deployed from the space station, thus it has to meet all the ISS requirements,” said Professor Periklis Papadopoulos, who also works at NASA Ames Research Center and served as a technical advisor on the project. “This has not been done before. Some of those requirements we had to help them define since there was no precedence.”

Normally, projects that are sent to the International Space Station take four and a half years to complete, said graduate student and system engineer Ali Guarneros Luna, but TechEdSat was completed in about nine months. The student team was responsible for designing and integrating the cube satellite’s system, as well as performing various tests and making sure it passed the standards of both the International Space Station and NASA.

In a NASA news release, Andres Martinez, program manager for Small Spacecraft Payloads and Technologies at Ames, said TechEdSat “will allow a group of very talented aerospace engineering students from San Jose State University to experience a spaceflight project from formulation through decommission of a small spacecraft.”

If this mission is successful, then it may lead to future cube satellites with a similar communication system.

Kevin Jordan and colleagues in flight simulator

SJSU Receives $73.3 Million Award to Participate in NASA Research

Kevin Jordan and colleagues in flight simulator

Kevin Jordan (front) with Tom Prevot (back left) and Vern Battiste (SJSU Research Foundation photo).

Cooperative Agreement Seeks to Enhance Safety and Efficiency of Air and Space Travel

Contact: Pat Lopes Harris, SJSU Media Relations, 408-656-6999

SAN JOSE, Calif., — The NASA Ames Research Center in Mountain View, Calif., has selected San Jose State University Research Foundation for a five-year, $73.3 million cooperative agreement to participate in the development of systems for improving the safety and efficiency of air and space travel. NASA scientists, along with SJSU faculty members and graduate students, will collaborate on this effort, funded by the largest federal award in SJSU history. The principal investigator will be Professor of Psychology and of Human Factors and Ergonomics, Kevin Jordan.

“San Jose State University is both proud and grateful to be selected to partner in Human System Integration Research at NASA Ames,” Jordan said.  “We are proud of the many accomplishments during our 26-year collaboration.  We are grateful for the opportunity to build on that collaboration to meet the design challenges of initiatives such as the Next Generation Air Transportation System and the Space Launch System. We are well positioned to face those challenges and we are committed to partnering with Human Systems Integration researchers in advancing NASA missions.”

This cooperative agreement will build upon Jordan’s 26-year association working with NASA to conduct research focusing on human factors in aeronautics and space exploration. A human factor is a physical or cognitive property that is specific to humans and influences functioning of technological systems.  Human Systems Integration Research studies how relationships between humans and machines can be optimized.

Under this cooperative agreement, San Jose State students and employees will work side-by-side with NASA scientists on a range of projects.  Examples include the Next Generation Air Transportation System, which seeks to modernize the nation’s air traffic system by increasing the capacity and safety of U.S. airspace and the Space Launch System, an advanced heavy-lift launch vehicle designed to take a crew vehicle, as well as important cargo, equipment and science experiments to Earth’s orbit and beyond.

The proposed projects will investigate the integration of unique human capabilities with future flight-deck (cockpit), air-traffic control, and mission planning and scheduling technologies. An important aspect of this award is that it will further SJSU and NASA’s efforts to provide graduate students with academic and professional training.

Dr. Kevin Jordan

In the past year, Jordan has overseen three cooperative agreements with NASA representing more than $10 million in funding and employing 75 researchers, including graduate students working toward degrees in psychology and human factors in ergonomics. Jordan has taught undergraduate and graduate courses in visual perception at San Jose State since 1984. During his career, Jordan has authored proposals resulting in over $125 million in funding to support collaborative research in aerospace human systems integration.

The San Jose State University Research Foundation is a 501(c)3 non-profit corporation established to enable and promote externally-funded programs that further SJSU’s comprehensive educational mission, impact, and public benefit. Each year hundreds of local, state, and federal agencies, businesses, and other organizations partner with the research foundation to engage SJSU faculty and other university specialists to perform basic and applied research, public service and community projects, consulting, and other specialized educational activities impacting the region, the nation and the world.

San Jose State — Silicon Valley’s largest institution of higher learning with 28,000 students and 3,190 employees — is part of the California State University system. SJSU’s 154-acre downtown campus anchors the nation’s 10th largest city.

SJSU in the News: Physics Professor Describes Discovery of Two Earth-Size Exoplanets

SJSU in the News: Physics Professor Announces Discovery of Two Earth-Size Exoplanets

SJSU in the News: Physics Professor Describes Discovery of Two Earth-Size Exoplanets

“In the cosmic game of hide and seek, finding planets with just the right size and just the right temperature seems only a matter of time,” said Natalie Batalha, Kepler deputy science team lead and professor of astronomy and physics at San Jose State University (NASA image).

NASA: Earth-size planets, Kepler-20e and Kepler-20f, discovered

Originally published by The State Column Dec. 20. 2011.

NASA’s Kepler mission trumpeted the discovery of several Earth-size planets circling a sun-like star outside our solar system Tuesday. While Kepler-20e and Kepler-20f (the newly discovered, Earth-size planets) are too close to the sun-like star to be in the “habitable zone,” where the formation of liquid water is possible on a planet’s surface, they are the smallest exoplanets (planets outside our solar system) ever validated around a sun-like star.

For NASA, the monumental discovery is the next milestone in the ongoing search for Earth-like planets. According to a NASA press release, the two Earth-like planets are believe to be rocky. Kepler-20e is a bit smaller than Venus or 0.87 times the radius of Earth. However, Kepler-2of is slightly larger than Earth or 1.03 times the radius of Earth. The Earth-size plants are part of a five-planet system named Kepler-20. Kepler-2o is roughly 1,000 light-years away from Earth in the constellation Lyra.

NASA reports that Kepler-20e circles a sun-like star every 6.1 days, while Kepler 20f orbits the same star every 19.6 days. Both of the Earth-size planets are similar to Earth in size only. The short orbits of the Earth-size planets corresponds to extremely hot and uninhabitable conditions on the planet. For example, Kepler-2of (8000 degree Fahrenheit) is similar to the planet Mercury as far as temperature is concerned. However, Kepler-2oe is even hotter (1,400 degrees Fahrenheit). Kepler-20e would melt glass.

“The primary goal of the Kepler mission is to find Earth-sized planets in the habitable zone,” Francois Fressin of the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, lead author of a new study published in the journal Nature, said in a NASA press release.

“This discovery demonstrates for the first time that Earth-size planets exist around other stars, and that we are able to detect them,” Mr. Fressin added.

The Kepler-20 system has other planets that are not Earth-like in size. Three of the other planets are bigger than Earth, but tinier than Neptune. NASA reports that Kepler-2ob, Kepler-20c and Kepler-2od, circle a sun-like star every 3.7 days, 10.9 days and 77.6 days. Additionally, all five planets in the Kepler-20 system have orbits that are similar to Mercury’s orbit. The planets of the Kepler-20 system orbit a star that is a bit smaller and cooler than the sun.

NASA also reports that the Kepler-20 system has a strange arrangement. In our solar system, rocky planets circle close to the sun, while large, gaseous planets circle farther out. However, in the Kepler-20 system, the planets are positioned in alternating size.

“The Kepler data are showing us some planetary systems have arrangements of planets very different from that seen in our solar system,” Jack Lissauer, planetary scientist and Kepler science team member at NASA’s Ames Research Center in Moffett Field, California, said in a NASA press release.

“The analysis of Kepler data continue to reveal new insights about the diversity of planets and planetary systems within our galaxy,” Mr. Lissauer added.

While scientists are not sure why the Kepler-20 system is arranged the way it is, they do not believe that the planets originated from the locations they are in now. According to NASA, scientists believe that the planets were constructed a greater distance from the sun-like star than they are now and eventually moved closer.

The Kepler space telescope looks for planets and possible planets by looking at “dips” in the brightness of more than 150,00o stars to reveal planets that are “crossing in front, or transiting, their stars.” After three transits, the Kepler science team knows that a planet has been discovered.

The Kepler science team deploys ground-based telescopes and the Spitzer Space Telescope to examine discoveries on possible planets that are located by the spacecraft. However, the star field that Kepler examines in the constellations Cygnus and Lyra can only be seen from ground-based observatories in the spring, summer and early fall. The data from the ground-based telescopes and the Spitzer Space Telescope help scientists confirm the discovery of planets.

Astronomer utilized a computer program called Blender to confirm the discovery of the Earth-size planets, Kepler-20e and Kepler-2of. Blender used simulations to determine whether other “astrophysical phenomena” were disguised as planets.

Back on December 5th, the Kepler team announced the discovery of Kepler-22b. Kepler-22b was found in the habitable zone of its parent star.

“In the cosmic game of hide and seek, finding planets with just the right size and just the right temperature seems only a matter of time,” Natalie Batalha, Kepler deputy science team lead and professor of astronomy and physics at San Jose State University, said in a NASA press release.

“We are on the edge of our seats knowing that Kepler’s most anticipated discoveries are still to come,” Ms. Batalha said.

image of blue and green planet in space

Physics Professor Announces Discovery of Potentially Habitable Planet

By Pat Lopes Harris, Media Relations Director

As Kepler deputy science team lead, Associate Professor of Physics and Astronomy Natalie Batalha joined NASA to announce today the mission has discovered its first planet in the habitable zone of another star. The habitable zone is the region around a star where liquid water could exist on a planet’s surface. Kepler also has discovered more than 1,000 new planet candidates, nearly doubling its previously known count.

“The tremendous growth in the number of Earth-size candidates tells us that we’re honing in on the planets Kepler was designed to detect: those that are not only Earth-size, but also are potentially habitable,” Batalha said. “The more data we collect, the keener our eye for finding the smallest planets out at longer orbital periods.”

The Kepler Mission, NASA Discovery mission #10, is specifically designed to survey our region of the Milky Way galaxy to discover hundreds of Earth-size and smaller planets in or near the habitable zone and determine the fraction of the hundreds of billions of stars in our galaxy that might have such planets.

Read more.