Thursday, March 5, 2020

Metabolic and genetic basis for auxotrophies in Gram-negative species

By Yara Seif

While some bacteria survive independently, others reduce their metabolic expenditures by utilizing the nutrients available to them in their environment. These bacteria choose to adapt the concept of simple living or “less is more,” meaning one can survive on minimal requirements (we could definitely learn from them). Auxotrophy, a.k.a nutritional dependencies, are a characteristic of host adaptation. They are hard to characterize experimentally because there are too many nutrients to choose from, and also because they differ from one strain to another.

In a study published Mar. 5 in PNAS, we develop a computational workflow that uses both flux balance analysis and comparative genomics to predict nutrient requirements de novo and from sequences alone.

In our workflow, we compare the gene content across several strains of bacteria, and build metabolic networks tailored to each genetic background. Next, we simulate for growth on a minimal medium, and when that cannot be achieved, we run our algorithm called AuxoFind, to search for possible nutrients that would restore growth in silico.

Metabolic networks were tailored to the gene content of different bacteria and nutrient dependencies were predicted and validated experimentally. Image courtesy of Systems Biology Research Group

We find that when the same gene is missing, the nutrient requirements change across species, because they have different metabolic networks and combinations of alternative pathways. We also observed that the absences are manifested as a result of a large range of genetic modifications going from simple and small mutations (like single nucleotide polymorphisms) to large and complex genetic changes (whole genome rearrangements and multi-gene deletions).

The significance of this work is as follows:

Patients with certain diseases (such as Crohn’s disease or cystic fibrosis) tend to be chronically infected with bacteria. Over time, these bugs become more vicious because they slowly adapt to the in vivo environment. Understanding how these adaptations occur is a first step towards devising therapeutic solutions.


Yara Seif is a UC San Diego bioengineering Ph.D. student. As a member of Bernhard Palsson's Systems Biology Research Group, she studies the metabolism of bacterial strains as well as the evolution of metabolic traits across strains especially in relation to their lifestyle. Her research so far has included multi-strain genomic and metabolic analysis of gram-negative strains using a combination of constraint-based metabolic modeling, comparative genomics and machine learning.

Tuesday, February 25, 2020

Barrett Romasko: structural engineer

 By Daniel Li

Barrett Romasko’s path in college has been full of exploration. Romasko, a senior majoring in structural engineering with a focus on aerospace structures, applied to UC San Diego without knowing much about the different applications of structural engineering, assuming it only involved civil engineering structures. His willingness to seek out new opportunities — through on-campus activities, classes, and internships — has been a contributing factor in helping him figure out his interests and goals for the future. 

On campus, Romasko is heavily involved in the UC San Diego Society of Civil and Structural Engineers (SCSE), which has three technical project teams that students can join to get hands-on structural engineering experience: steel bridge, concrete canoe, and seismic design. Romasko has been part of the steel bridge project team since his sophomore year –he was the team’s welding lead his junior year and is currently the project manager. 

The steel bridge project challenges students to design, fabricate, and construct a scaled model bridge that stays competitive in terms of the lightest weight, greatest stiffness, and fastest construction speed. The students start preparing their bridge each fall and bring it to the annual Pacific Southwest Conference each year to see how it stacks up to the competition.

The steel bridge team with their bridge.
“We start the design process in fall quarter, which generally consists of using a lot of design software and analysis,” Romasko said. “Winter quarter is dedicated to fabrication, so the team takes the design to a machining space and manufactures each component of the bridge. The last stage is construction, which is when we practice assembling each member of the bridge according to the regulations that we received in preparation for the competition.”

According to Romasko, the hardest part of the competition is getting all the components fabricated by the competition in April. That was compounded this year, as the team had to find a new location to fabricate their bridge, as the location they’d been using for 18 years was no longer available. Romasko and his co-project manager got to work and were able to come up with a solution.

Despite unexpected challenges, Romasko has enjoyed working on the steel bridge project the past three years. His favorite parts about steel bridge: the teamwork and hands-on learning aspect.

“I really like steel bridge because you get to apply what you learn in class to a real project and work with so many cool, motivated people,” Romasko said. “You also start to understand important industry concepts such as fabrication and tolerancing.”

Romasko encourages students to get involved in student groups as early as possible, and stresses the importance of finding organizations that are not only career focused, but also fun. 

“Joining the steel bridge project has introduced me to so many new people that I wouldn’t have met otherwise,” he said. “It has been a good way for me to make friends who share like-minded interests.”

In addition to their hands-on technical projects, SCSE organizes two main community outreach events each year: Seismic Outreach and Esperanza International. 

Members of the steel bridge team.
“Seismic outreach consists of us going to schools to teach elementary and middle school students about how to design for seismic safety and teach them about earthquakes,” Romasko said. “The goal is to get these students more interested in STEM fields. We also have another event where we go down to Rosarito in Mexico with an organization called Esperanza International, and put our engineering skills to use as we help build houses for the less fortunate.”

In addition to his involvement in SCSE, Romasko is a research assistant in Professor Machel Morrison’s lab, where he works on projects related to metallography and mechanics of materials. He’s also nabbed several internships over the summers, working at the Naval Surface Warfare Center in 2018 and General Atomics in 2019. 

“Internships are valuable because you can get direct experience in the industry,” Romasko said. “The internships that I have done really allowed me to see what I could do with my major and what I don’t want to do with my major. For example, at General Atomics, I was a manufacturing engineering intern; after the summer, I realized that although it was a great learning experience, I wouldn’t want to do it as a career. I feel that it is important for everyone to explore different areas to find what they’re most passionate about, and even more importantly, to find what they aren’t passionate about.”

Romasko came to UC San Diego thinking that he was going to follow the civil structures route in the structural engineering department, but during his internship at the Naval Surface Warfare Center, he realized that aerospace structures were more interesting to him. Without that internship, Romasko said he fears he would never have changed to the aerospace structures focus.

Romasko is returning to UC San Diego to complete a master’s degree in structural engineering this fall. In the future, he hopes to work abroad for a couple years, either in Australia, Europe, or New Zealand.

“I would love to work outside of the United States for two to three years doing something related to aerospace structures,” Romasko said. “One of my dream companies to work at is Virgin Galactic, which specializes in developing commercial spacecraft.”

Friday, January 31, 2020

Students Enspire the next generation of engineers

By Daniel Li

More than 180 high school students came to UC San Diego on Monday, Jan. 27 for Enspire, an annual daylong event for students to learn about different engineering disciplines and how to fund their college education. The event, held at Price Center Ballroom East, was organized by the Triton Engineering Student Council.

Computer science professor Christine Alvarado kicked off the event as the keynote speaker. Alvarado discussed her research in supportive learning and emphasized the importance of not giving up, even if the field might seem too hard. 

“It's not always easy to come into college studying engineering or computer science, but it can be super rewarding and you do not need experience coming in to succeed,” Alvarado said. “Many of our students who come into UCSD as computer science and engineering majors have never taken a programming class before.”

Financial aid counselor Rashinda Hutchinson took the stage next and spoke to students about the different types of aid packages. She also educated students on important deadlines for the FAFSA application, strongly encouraging them to start in October of their senior year.

In an effort to introduce students to the myriad of engineering-related student organizations at UC San Diego, TESC invited two panels onto the stage. The first panel was focused on diversity, with representatives from Women in Computing, the Society of Hispanic Professional Engineers, National Society of Black Engineers, and Society of Asian Scientists of Engineers. Meanwhile, the second panel made up of representatives from different engineering-specific organizations, including electrical engineering, aerospace engineering, chemical engineering, computer science, and bioengineering.

After the presentations, the students were broken up into groups of six to participate in four
workshops: AIAA Bottle Rocketry Activity, HKN Circuitboard Challenge, TritonXR VR Demo, and HKN MAE activity. According to TESC outreach lead Nicholas Fu, these workshops were designed to showcase the different aspects of engineering, ranging from mechanical to electrical and computer engineering.

“We wanted to show students how to problem solve in interactive ways, without an instruction set,” Fu said. “We believe that the students did great and were pleasantly surprised about how many ingenious ways they solved issues.”

Isiah Encakado, a senior from Mountain Empire High School, came to the event to learn more about engineering opportunities at UCSD and interact with college students. He hopes to pursue a degree in computer science in college. 

“So far, I’m really glad I came and everyone has been extremely welcoming,” Encakado said. “I am definitely learning new concepts and skills from these workshops”

According to Fu, the planning team, which consisted of three committee members and several board members, started preparing in the summer to go over big picture ideas and logistics. The hardest part: making sure all of the dates and numbers were set.

“We had some difficulty with getting the exact number of students and then telling the organizations we were working with how much they should bring for their activities,” Fu said. “We definitely learned a lot about the merits of finalizing attendance numbers early and then staying firm after.”
Fu’s favorite part about running Enspire is working closely with high school students during the interactive workshops.

“It really helped me realize why we worked so hard the many weeks before,” Fu said. “I loved seeing how the students worked together and what they were able to do.”

Monday, December 9, 2019

Researcher by day, Ironman by night

By Daniel Li

Beril Polat
Not many people have the willpower to complete a 12-hour race consisting of a 2.4-mile swim, 112-mile bike and 26.2-mile run. Not many have the smarts and stamina to earn a doctorate degree in nanoengineering. But the number of people capable of doing both simultaneously is miniscule. 

For fourth-year UC San Diego nanoengineering Ph.D. student Beril Polat, training for Ironman competitions and her graduate school work go hand-in-hand.

“The main reason why the Ironman is so challenging is there’s also a mental aspect to it,” Polat said. “And that kind of challenge helps a lot in grad school because you get a lot of stress from work, deadlines, and publishing. After finishing an Ironman, I came back to lab two days later, and there were some small problems we were facing. I remember thinking that this was so small compared to what I just accomplished so I wasn’t going to let it bother me; I didn’t let it get into my head and tried to solve it.”

Polat completed her undergraduate and master’s degrees in chemical engineering at Johns Hopkins University before matriculating to UC San Diego to pursue a Ph.D. in nanoengineering. She’s currently a student in Professor Darren Lipomi’s nanoengineering lab, where she develops tattoo sensors to help patients with neck cancer monitor and regain their ability to swallow. 

Polat is a graduate student in Professor Darren
Lipomi's nanoengineering lab.
 “The reason why we are targeting neck cancer is because after patients get chemotherapy, their swallowing may be affected as a side effect,” Polat said. “We are trying to make a tattoo sensor that they can apply themselves at home instead of coming to the hospital very frequently. They can apply it and that data on their muscle strength will be sent through their phones to physicians so they can monitor it.”

Outside of lab, Polat is an avid member of UC San Diego’s triathlon club. She was introduced to triathlons during her first year at UC San Diego after meeting members from the triathlon club. She recalled being hesitant at first about joining because of her busy schedule, but then fell in love with the team and competitive nature of the sport.  

“In college, I swam varsity for two years at Hopkins, but the stress level was too high for that so I quit,” Polat said. “Because of that, I didn't compete in a sport for years, which kind of rubbed me the wrong way. After coming to triathlon practices at UCSD, the feeling of competing came back to me and it felt amazing.”

Polat recently competed in an Ironman Triathlon this past summer in Canada. The Ironman is considered the ultimate triathlon and test of endurance.

“This was my second time competing in an Ironman Triathlon,” Polat said. “I competed in it for the first time with my boyfriend the summer of 2018. I signed up eight months before the race day and trained every day. My goal is to do at least one every year.”

According to Polat, she starts her day at 6:30 am with training every day. Her morning workouts usually consist of cycling for an hour and running three miles. On the days where Polat trains twice a day, she has a swim workout in the evening at Canyon View pool on campus. 

“I try to train at least once a day, sometimes twice,” Polat said. “I usually go in the early morning because I want to keep a schedule where I am at work from 9 am to 5 pm. I'm not forced to go every day, but I know that if I want to get better and faster, I need to train that much.”
Polat during the 26.2-mile run, the last leg of an
Ironman Triathlon.
Polat appreciates how competing in triathlons has been a healthy escape from her hectic life in graduate school. Her most important takeaway from this experience: time management. 

“I recommend anyone to really commit to a non-school related activity, whether it be a sport, music, or art,” Polat said. “It really keeps you grounded and teaches you how to keep track of your goals. At times, it can definitely be a challenge because it’s hard to juggle both at once. However, if it wasn’t challenging I wouldn’t do it.”

In the future, Polat envisions herself shifting gears and working in industry. Although she enjoys the process of conducting research at her lab, Polat has learned that she prefers having a faster turnaround time for products that she works on.  

“When you conduct research in a lab, it can take a long time to get something out,” Polat said. “You can publish it but getting it into the market is very hard and requires a lot of steps. I like the industry aspect of being able to see people use something that I worked on and designed.”

Her next challenge? Ironman Maryland in September.

Friday, November 1, 2019

5th annual SD Hacks draws hundreds of student participants

By Daniel Li

More than 750 students participated in the 5th annual SD Hacks.
Photo credit: Shirley Guo, Triton Engineering Student Council

For 36 hours straight, 143 student teams crammed together at UC San Diego’s RIMAC Arena to participate in the fifth annual SD Hacks hackathon

Held from Oct. 25-27, SD Hacks is an intercollegiate hackathon in which students come together to tackle a given problem by developing technical solutions. The event, organized by the Triton Engineering Student Council, was also sponsored by ten companies and organizations, including the Naval Information Warfare Center, Northrop Grumman Corporation, and Activbody. A total of 435 students participated this year.

Hackers were asked to develop projects that fell into one of the three main tracks: Sustainability, Education, and Health and Wellness. Attendees were also encouraged to participate in various challenges set by SD Hacks sponsors. 

After two hours of judging on the last day, a trio of students from Harvey Mudd College-- Matthew Krager, Alfredo Gomez, and Alice Chi-- emerged as the overall winners of the hackathon. The team developed a tool called EverGreen, which aims to analyze and reduce the carbon emissions of code. 

“Given an expected amount of traffic and set of computer specs, EverGreen is able to capture the environmental impact that a programmer's code will have by using various metrics such as the carbon emitted in the average lifespan of a car,” the EverGreen project submission states. “Since many of today's large computations are done on the cloud, we have provided users with various industry standard AWS instance type-based architectures.”

They received Apple iPads, Bose SoundLink wireless headphones and an Amazon giftcard for their 1st place prize. 

For some students, it was their first time participating in a hackathon. Second-year UC San Diego students Vincent Tran, Steven Liu, Isabel Suizo and Vasundhara Sengupta developed a live-streaming app called 
Steven Liu, Vasundhara Sengupta, Vincent Tran, Isabel Suizo
Photo by Daniel Li

“The concept behind is that you're walking around on the street late at night and things could be a little dangerous,” Tran said. “You don't want to call 911 but you might want to let a friend know, and currently your options are to call or text them.  But that might hinder your ability to get out of a dangerous. If something does happen, you're not gonna be able to whip out your phone and draft up this text. So that's the issue we're trying to solve.” 

Despite having to start over on their project 12 hours into the event, Liu appreciates his team’s positive attitude and how he was able to learn new programming languages. 

“I would describe this weekend as a roller coaster,” Liu said. “Coming in, we were all super ambitious and ready to build something. And as it turns out, development is not always so easy.”

Third-year UC San Diego computer science students William Vuong, Howard Lin, Jack Song and fourth-year student Kevin Vildosola teamed up to create Stutter, an interview prep service that analyzes and provides feedback on how people perform during interviews. 
Jack Song, Howard Lin, William Vuong, Kevin Vidosola
Photo by Daniel Li

 “Ultimately, as college students, we always interview for internships or jobs, but never receive feedback,” Vuong said. “We wanted to give people a way to better prep for interviews so that we can all crush future interviews.”

Vildosola is grateful that he was able to learn from other students who had more experience and knowledge in development. 

“My experience at SD Hacks was honestly amazing,” Vildosola said. “It’s so rewarding because I never imagined I’d be at a stage right now where I could be talking about an app that I helped create.”

According to SD Hacks director and computer science student Jimmy Dang, preparations for SD Hacks started in June 2019, after the HackXX hackathon. The organizing team comprised of 20 members from the HackXX team and Triton Engineering Student Council. Dang explained that the hardest parts of the planning process were attracting sponsors and finalizing day-of event logistics. 

“There were a lot of moving parts in a lot of different areas of the hacking venue, especially moving people from RIMAC arena to Mandeville,” Dang said. “We also had a lot of rebranding to do, given it was our 5th anniversary and we wanted to make sure it was the best hackathon we’ve ever held.”

His favorite part about SD hacks: interacting with both sponsors and hackers during the event. Dang emphasized that the hackathon would not be possible without the collaboration among companies, student organizations, volunteers, judges and mentors. 

“Being able to interact with the attendees at our event made me feel like all of the effort that was put in, completely worth it,” Dang said. “Seeing people satisfied and enjoyed with our event made me feel satisfied with the work that I, as well as the entire team, put in over the course of four to five months.”


First Place Overall: EverGreen (Matthew Krager, Alfredo, and Alice Chi)

Second Place Overall: Corssary (Jacob Rothman, Jonathan McGowan, Roderick Nappier, and Dhanush Karthikeyan)

Third Place Overall: Ribbit (Sarah Ekaireb, Spencer Congero, Sarah Jung, and Alex Yu)

Health & Wellness Category: Recipe 101 (Xiaolan Huang, Yitian Wang, Moon Jiao, Duolan Ouyang)

Sustainability Category: EcoEat (Spencer Churchill, Moses Lee, Sophia Song)

Education Category: Virtus (Sabeel Mansuri, Subhash Ramesh, Nikhil Pathak, Ayush Shukla)

A full list of winners can be found at

Friday, October 25, 2019

Association for Computing Machinery attracts over 500 students at its fall kickoff

By Daniel Li

More than 500 students showed up for ACM's Fall Kickoff.
Photos courtesy of ACM

This year, a new student organization has been rapidly gaining momentum at UC San Diego: the Association for Computing Machinery (ACM). 

ACM’s Fall Kickoff, which was held on Sept. 29 at Price Center East Ballroom, attracted a whopping 500 students, with the line spanning from the ballroom entrance to Library Walk. In the first month since its launch, the club has also hosted over 15 professional and social events. 

According to founder and president Antony Nguyen, a fourth-year computer engineering student, ACM is an international organization for computing catered towards engineers, designers and entrepreneurs. Just last week, the club introduced “Hack School,” a workshop series aimed to teach students the basics of Full Stack Web Development. 

“Our events are geared towards the field of computing and there's so many different areas we hope to explore, including software engineering, as well as mobile app, web and game development,” Nguyen said. “We also host a variety of social events to build a community so that everyone can get to know each other.”

He got the inspiration to start ACM at UC San Diego in January 2019 after stumbling upon UCLA’s chapter, which started four years ago and boasts a membership of over 1000 people. In the subsequent months, Nguyen and several friends teamed up to start a chapter at UC San Diego. 

Before launching the club, the group met over the summer to think of ways to differentiate ACM from the abundance of engineering organizations on campus; one important aspect was how to define membership. 

Students on the ACM leadership board rep the group and its
signature diamond logo. 
“I remember as a first- and second-year student, I joined some clubs and people would ask me ‘Are you part of this club?” Nguyen said. “And this was hard for me to answer because I just show up to events and many clubs really don’t define what it means to be a member.”

Vice President of Membership Kendall Nakai, a second-year computer engineering student, explained that the chapter prides itself on being member-centric and has a membership portal where students can track their progress within the organization.

“We wanted members to have a way to know how far they’ve come in the organization,” Nakai said. “By showing up to events, members can get incentives, such as priority access to networking events. I think it’s important to reward the people who consistently show up to all events.”

Unlike most student organizations, which use Slack as their main method of communication, ACM adopted Discord, a text-messaging platform popular in the gaming community. Nguyen said that this choice was deliberate, as the club hopes to develop more personal connections with its members. 

“Discord is a big reason for our success,” Nguyen said.  “By summer we had over 100 incoming first-years who hadn't even started school on our Discord. Nowadays, the discord is used on a daily basis; people play games with each other, give career advice and just talk about life.” 

Nguyen also attributes the large turnout to the club’s advertising efforts. The team branded itself as part of “the largest computing organization in the world” and distributed flyers across campus. He added that having the entire executive board well-connected within the engineering community gave them a tremendous advantage. 

ACM members on a hike just blocks away from campus.
“Having connections before starting your organization is extremely important,” Nguyen said. “The moment we launched our kickoff, we sent personal invitations to our event page on Facebook. It's like a giant chain effect; people start pressing ‘going,’ and then their friends on Facebook will see it too.”

Nguyen stressed the main benefit of ACM is that it’s tied to an international organization, introducing students to a large, diverse network of people. 

“Having a strong network is what gets you jobs at companies, big or small,” Nguyen said. “We can give students connections that otherwise might be harder to get from other clubs.”

Thursday, October 10, 2019

MEMS Q&A with Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering

“As a MEMS practitioner for almost 30 years, I fully understand the need to focus at the device level to ensure that the MEMS design meets SWAP (Size, Weight And Power) and other requirements,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “But I truly believe that MEMS designers must learn to think more about subsystem and system issues, since the future of MEMS will be won by those who cannot only design the device right, but who can design the right device. By taking a much more market- and system-oriented approach to MEMS design thinking, companies in this industry will realize greater success.”

portrait of Albert P. Pisano, Dean, UC San Diego Jacobs School of Engineering
Read the full Q&A with Albert P. Pisano and Nishita Rao, marketing manager for technology communities, at SEMI

The Q&A was put together in advance of Pisano's October 24 closing keynote presentation, MEMS and Systems in the Digital Future, at MEMS & Sensors Executive Congress, October 22-24, 2019, at Coronado Island Marriott Resort & Spa in Coronado, Calif.