News

By Shaharyar Lakhani

SynCell 2020, the International Conference on Engineering Synthetic Cells and Organelles, will be held from May 11th through May 14th, 2020 in Santa Fe, New Mexico (https://syncell2020.unm.edu). The conference will focus on the challenges and opportunities in synthetic cell technology, or in other words making cells from scratch! Topic areas for the main program will include creating synthetic cells and organelles, spatial and temporal organization of these cytoplasmic structures, signaling and circuits, molecular machines, mechanics, motility, and the implications of synthetic cell technology. SynCell will feature talks from world leaders in synthetic biology from premier American and German universities and labs, including our very own Dr. Andy Ellington from the University of Texas at Austin, who will be discussing how DNA nanotechnology and protein engineering can impact the de novo development of cells. Talks will range from the engineering of biomolecular systems (Matthew Lakin, University of New Mexico) to the potential applications and simulations of these systems (Kate Adamala, University of Minnesota). An evening poster session and other dedicated times for free-form discussion are also planned. A featured translational speaker, Mike Jewett, will explore issues related to working with industry on the commercialization of synthetic cell technologies, and an industrial forum is planned for after Dr. Jewett’s talk. Finally, the first day of the conference consists of an interactive educational component for students and aspiring researchers.

By Shaharyar Lakhani

On August 23rd, 2019, many notable practitioners of synthetic biology from the University of Texas at Austin got together and shared their expertise with students, researchers, and administrators, all as a part of UT Synthetic Biology Day 2019. Lectures from professors at the University paired with an interactive poster session made the audience aware of the cutting edge developments happening in labs right here on campus. Amongst the many remarkable feats revealed by the synthetic biologists of UT-Austin, Dr. Hal Alper showed yeast that were so far (produced so much lipid) that they could float on water (http://www.che.utexas.edu/alper_group/); Edward Marcotte showed how bioinformatics could be used to convert a drug used to treat worms in elephants into a potent anti-cancer agent (www.marcottelab.org), and how the yeast genome could be progressively humanized into “Saccharomyces sapiens”; and Sean Leonard from the Barrick (http://barricklab.org) and Moran (http://web.biosci.utexas.edu/moran/) labs showed how engineering the bee microbiome could help prevent colony collapse. Furthermore, a panel discussion highlighted the contributions of industry, clinicians, and the security community towards the future of synthetic biology.

The international DNA nanotechnology meeting, DNA25, was held this year in Seatlle, Washington on the University of Washington campus. This is the annual gathering of researchers interested in all aspects of DNA computation, and this year there was a focus on the use of DNA as a potential alternative to silicon as an information storage medium.  Surprisingly, it may soon be cheaper to store archival data as nucleotides (GATC) rather than as digital flips in a memory core.  Key issues that remain to be solved include how to access and easily read out the data, a problem that was considered in depth by another University of Texas at Austin researcher, David Soloveichik of the Electrical and Computer Engineering Department.  In addition to delivering a talk on manipulation xenonucleic acids (XNAs) for computational applications, Dr. Ellington participated in a panel on the future of the field (see picture). This panel included Dr. Ned Seeman, widely regarded as the founder of DNA nanotechnology; Shelley Wickham of the University of Sydney; Anne Condon, from the University of British Columbia; and William Shih of the Wyss Institute at Harvard.

Read More About DNA25

On August 1 & 2, the Engineering Biology Research Consortium (EBRC) held a symposium in Washington D.C. titled ‘The Convergence of Engineering Biology & Data Science: Understanding Risk and Mitigation Options’. The discussion was focussed on how computer and data science is impacting security in the field of biological engineering, and strategies to mitigate these issues. Talks were wide-ranging, from field overviews (Richard Murray, Caltech) to technical contributions (Lance Stewart, Center for Protein Design UW). Graduate student Austin Cole represented the Ellington Lab and a new start-up company, AI Protein Solutions, and presented a talk titled “Structure Based Machine Learning for Protein Engineering.” The talk was an outgrowth of novel neural network analyses of protein structure and stability, but was canted towards the possibilities inherent in using AI to predict and counter emergent biothreats. Speakers were drawn from top biological engineering laboratories in both academia and industry. The audience was composed entirely of Government stakeholders from a variety of agencies. Attendees discussed strategies that might be used to preemptively identify biological threats as well as how better risk assessments might be carried out.

On July 30, Dr. Ellington visited Cold Spring Harbor Labs (CSHL) in New York to deliver a lecture to the Synthetic Biology Summer Course, “The Tenuous Balance Between Systems and Synthetic Biology.” Because of the centrality of both systems and synthetic biology in the Center for Systems and Synthetic biology (duh), Dr. Ellington could bridge between Ed Marcotte’s fundamental work on phenologs and yeast humanization to his own work on augmenting the genetic code and developing orthogonal control systems for organisms. The CSHL course is a mainstay of students learning to enter the field of synthetic biology, and the diversity in backgrounds was fascinating. The beer was even better (still not sure about the raspberry ale).

Read more about CSHL

Synthetic biology is a powerful discipline that combines the scientific insights of biology with the translational strengths of engineering to produce new and useful biological systems. The University of Texas at Austin has a number of extraordinary practitioners of this discipline, and on August 23 from 9 AM to 4:30 PM, they’re going to get together in the Engineering Education and Research Center (EER 0.904) to share their expertise with other students, researchers, and administrators from around the campus. Amongst some of the notable achievements that will be discussed are the use of microbes being engineered in the Barrick Lab to protect agriculture, the modification of molecular complexes in CRISPR-Cas systems by the Finkelstein Lab to improve biochemical activity, and the development of proteins at the Maynard Lab that redirect immune cell activities to better defend the body from infectious diseases. In addition to these projects, the symposium will showcase various other cutting edge developments that are actively changing the world we live in. UT Synthetic Biology Day 2019 is something you don’t want to miss!

At the end of 2018, Dr. Andy Ellington and Dr. Eric Anslyn from the University of Texas at Austin, among 13 other scientists, were awarded a grant from NASA totaling nearly $7 million to continue research in detecting extraterrestrial life. This comes as a part of NASA’s Astrobiology Program, which is working to find life on neighboring planets using what’s called LAB, the Laboratory for Agnostic Biosignatures. In June 2019, Dr. Ellington and Dr. Anslyn attended AbSciCon, NASA’s Astrobiology Conference, and discussed efforts to detect these “agnostic biosignatures of life”. 

“The signals we are looking for are chemicals that are so complex that they could only have been created by some form of life,” says Dr. Anslyn. Really, any type of signature could be possible, although proteins and nucleic acids like that of humans are unlikely. “Since we don’t know what type of signal to expect, we need an agnostic method to detect life,” he further explains.

NASA also announced its “Dragonfly Mission” and presented the mission’s commander at AbSciCon 2019. Dragonfly’s goal is to create a probe that will launch in 15 years to Titan, one of Saturn’s moons, will take 8 additional years to reach its destination, and look for hints of life. While NASA is working to engineer this complex machinery, Dr. Ellington, Dr. Anslyn, and others are working together to develop chemical tests that NASA’s machinery would implement. In the near future, we hope to discover more about our neighboring planets, and what inhabits them.

Read more about AbSciCon

Mosquitoes are known for housing a variety of nasty diseases, from Zika to dengue to yellow fever. As the weather begins to warm up, we want to enjoy the warm Texas sun. Unfortunately, so do the mosquitoes. Since these blood sucking creatures carry a variety of diseases, they make it difficult to enjoy the summertime. Mosquitoes that are infected with the bacteria Wolbachia however, have a reduced ability to transmit viruses to people, such as Zika or dengue. Dr. Sanchita Bhadra of the Ellington Lab in collaboration with Dr. Tim Riedel and his students in the DIY Diagnostics Freshman Research Initiative stream have developed an easy way to test mosquitoes to find out if they carry Wolbachia within tens of minutes, using LAMP-OSD. 

Earlier this year, Drs. Dagne Duguma and Mustapha Debboun from the Harris County Mosquito and Vector Control Division of the Texas Department of Health visited UT Austin to observe a demo of the Wolbachia test. They talked in detail with Dr. Bhadra and DIY Diagnostics undergraduate researcher, Simren Lakhotia, regarding application of this LAMP-OSD technology to facilitate vector surveillance in Harris County. “The representatives from Harris County were visiting us because they are interested in using our LAMP-OSD assay to test for Wolbachia in mosquitoes,” explains Dr. Bhadra. “We are getting ready to send them 100 Wolbachia tests, with which they will test mosquitoes collected from various regions in Harris County” she further stated. If successful, this pilot test will set the groundwork for developing and applying a larger suite of molecular testing methods for vector surveillance. By learning more about the environment around us, we can begin to address the public health problems plaguing us.

Dr. Eric Anslyn and Dr. Andy Ellington were present at the annual meeting on the Howard Hughes Medical Institute (HHMI) compound in Chevy Chase, Maryland. The meeting was hosted by the HHMI Professors Program, a program empowering research scientists to extend engaging research opportunities to undergraduate students and improve science education. They presented both a lightning talk (Dr. Ellington) and chalk talk (Dr. Anslyn) on their conjoined efforts to develop professional and entrepreneurial education for undergraduates. Specifically, they presented their program known as Translational Research Initiative Professional (TRIP), which gives undergraduate chemistry majors first-hand experience of what it is like to be a graduate student in chemistry, as well as a close look at the lifestyle and career of chemistry professors. 

In addition to presenting their own efforts, they also interacted with a wide array of other Hughes’ Professors, who were promoting projects ranging from increasing the representation of underrepresented minorities in astronomy (Keivan Stassun, Vanderbilt) to carrying geoscience back to students’ home communities (Julia Clarke, University of Texas at Austin) to veterans’ involvement in the sciences (Dr. Marla Geha, Yale). Since the program began in 2002, sixty-nine scientists have been named HHMI professors, working to support students in their path to STEM related careers. 

Read more about the HHMI Professors Program here

In order to train the scientists of the future, they should be exposed to cutting edge approaches now.  This of course is what a modern research University does; it provides undergraduates with access to key thought leaders and research resources that enable STEM career paths to be built and taken.  But why wait until college to start this process? The TIDES program and the Freshman Research Initiative at the University of Texas offers research opportunities to high school students, placing them in labs for a summer experience through the High School Research Academy. This program has been placing students in the Ellington Aptamer FRI research stream for the past eight years, allowing the students to decide what projects and procedures to carry out. Additionally, the students have seen successes in iGEM science competitions, winning gold in 2015, as well as bronze in 2017 and 2018. Now, the Ellington lab has developed a program to bring high school students into research labs for longer internships that last through the entire academic year. As a result, in addition to early training and prolonged exposure to the sciences, the high school students will gain critical presentation skills from exhibiting their work in international competitions such as iGEM and Intel ISEF. By granting them additional time in the lab, these students are able to not only develop thorough research ability, but interact with local and global experts alike, allowing them to develop a network which they can leverage throughout their careers.