The sixth annual IEEE EMB (Engineering in Medicine and Biology) strategic conference was held in Maryland from November 20th through November 22nd of this year. The conference focused on Health Innovations, specifically POCT (Point Of Care Technologies), and provided a “strategic forum in which clinicians, industry experts, innovation experts, researchers and students will examine how to define unmet clinical needs and successfully travel along the innovation cycle towards commercialization and patient impact.” The main goal of this conference was for stakeholders to explore these technologies and collaborate to improve healthcare at an affordable cost. Dr. Ellington from the University of Texas was in attendance and gave a talk on “Synthetic Biology/Gene Editing’s Role in Diagnostics”. Dr. Ellington provided insights into the difficult task of reducing complex technologies to the bedside and beyond, where simplicity is more important than scientific novelty. In particular, he discussed how simple isothermal amplification and simple oligonucleotides probes (so-called LAMP-OSD) may be vastly superior to CRISPR-based methods for diagnostics.
By: Shaharyar Lakhani
The International Genetically Engineered Machine competition (iGEM) is now accepting applications for the 2020 cycle! The year-long in-depth program is in preparation for the annual synthetic biology competition where multidisciplinary teams are given a kit of biological parts, which they combine with parts of their own design to build new biological systems and operate them in living cells. These teams aim to use their creativity and innovation to help solve local problems using synthetic biology. This competition kicks off at the beginning of summer, and presentations of the new systems are held in the fall. The process will begin this December, where accepted students will generate an idea for their project. The upcoming spring semester entails a 1 credit hour course to give students the time and resources to brainstorm, develop their project, read background papers, contact people with expertise in the area, and to build upon their ideas.
This year’s batch of students on the UT iGEM team won a gold medal for the best measurement category at the iGEM Jamboree in Boston. They worked on a device that measures the amount of metabolic burden inside a cell. These burdens hinder the progress of synthetic biology because the cells don’t function like they are supposed to. The team’s “Burdenometer” measured the burden associated with 330 parts (including promoters, coding regions, terminators, ribosome binding sites, etc.) from iGEM distribution kits and found parts that could be replaced with a more stable construct. “However,” the team stated, “we are not just limited to these 330 parts; with this innovation, synthetic biologists can determine the burden of any genetic part that interests them!”
The deadline to apply to the UT iGEM team for the 2020 cycle is December 1st, 2019. Don’t miss out on this opportunity! (Apply here)
By: Shaharyar Lakhani
Earlier this year, Austin Cole, Raghav Schroff, Danny Diaz, and Dr. Ross Thyer developed a machine learning algorithm to predict the identity of functional amino acids in protein sequences with high accuracy (Speeding up Evolution using AI). They have now translated this technology into a company, AI Protein Solutions. Recently, the company and corresponding team of inventors was selected to be a part of the ICORPs Program of the National Science Foundation (NSF), which prepares scientists and engineers to get their products from the laboratory to the market. “The technologies that we as engineers come up with and the products we design are far short of a company,” explained Austin Cole. “The ICORPS Program introduced us to factors involved in taking our product and turning it into a commercial endeavor, such as finding competitors, reaching customers, and other business networking skills.” In 7 weeks time, the team flew around the country on 9 trips and ultimately interviewed 66 companies relevant to their product. These trips provided insights into many of the problems that AI Protein Solutions hopes to solve, and the team believes it can use the advanced neural network they have generated to improve the structure and function of enzyme catalysts for textile, agricultural, bioprocessing, and therapeutics applications. While the exact individuals and companies the team spoke with remain confidential, they found productive and active partnerships, and are in the process of starting work with them. “We came out of the program with a better understanding of how to bridge the gap between the business side and the technical side,” The experience gained through the ICORPs Program was invaluable, and according to Cole while “there is no business training for technical individuals, and while being tech savvy is important, learning about business mechanics is essential when making a company. While the quality of your product is obviously important, the trust that the company confides in you and the relationships that you build are most essential, since they will be trusting you to solve their problems.”
Project DREAM, led by Principal Investigators Dr. Carla Cruz (University of Beira Interior) and Dr. Andy Ellington (University of Texas at Austin) aims to mitigate the harmful side effects of anticancer drugs by using a unique nanosystem to target tumor cells and prevent healthy tissues from exposure to the otherwise toxic drugs. Recently, Dr. Cruz and Dr. Ellington were interviewed by a representative from the UT Austin Portugal Program (a major partnership program in between the Portuguese Foundation for Science and Technology and UT) regarding their unique approach and explained how an aptamer known as AS1411 could be modified to better carry drugs to tumors. “Previously, it was demonstrated that these aptamers can selectively deliver anticancer ligands,” Dr. Cruz said, such as acridine orange derivatives, and showed improved selectivity towards cancer cell lines. However, she continued, “moderate concentrations and long incubations were required to observe cytotoxicity.” In order to improve the selectivity and efficacy of the aptamers, they were conjugated to gold nanoparticles, which are preferentially internalized by tumor cells. Better cytotoxic effects were achieved with shorter incubation periods (2 days). The DREAM project ultimately includes researchers from two Portuguese laboratories (CICS-UBI and C2TN-IST), a public hospital (CHCB), a company (Labfit-HPRD) and the Ellington Lab from UT Austin, and overall the team hopes to move compounds towards clinical utility within 5 years via the COST Action program (a network for nationally funded research projects).
Our very own Professor Barrie Kitto from the Molecular Biosciences department was recently featured in a documentary about his former advisee and Nobel laureate, Jim Allison. The documentary, titled “Jim Allison: Breakthrough” is the true story of a “warm-hearted, stubborn man’s visionary quest to find a cure for cancer.” The film traces the remarkable life of Jim from his early days, and guides us to how he got where he is now. In the words of Dr. Kitto: “I had a chance to see the premiere at SXSW and it is a fine film (even though I have a very small part in it). It has already received a slew of positive reviews from major critics.”
If you haven’t gotten a chance to see it yet, grab a friend and go to the Regal Theater at Great Hills either today or tomorrow. For the trailer, showtimes and tickets, visit Regal Theaters. Happy viewing!
By: Shaharyar Lakhani
Everett Stone, a cancer researcher at the University of Texas at Austin, was recently featured in and episode of “Forged-in-Fire”, a series where experienced bladesmiths try to recreate some of the most iconic weapons throughout history. Stone even ended up taking a $10,000 check home as he was crowned champion of the bladesmithing competition. However, Stone’s path to this was rather unique.
Ever since he was 16, Everett Stone loved blacksmithing because of the way that he could solve problems hands-on, such as helping his horses with their sore feet due to the rocky ground. For 14 years after that, Stone had his own horseshoeing business. Stone later decided to attend college when he found an interest in medical science. Due to his background with animals, he planned on becoming a veterinarian, but he quickly fell in love with biological research and the potential discoveries that could come along with it. He went on to receive a B.A. in chemistry and biology from Drury University, and then headed to UT to get a Ph.D. in cell and molecular biology. Since then, he’s been a research assistant professor focused on creating new cancer drugs and immunotherapies.
In addition to being an assistant professor, Stone has helped found two biopharmaceutical startups: Aeglea BioTherapeutics and Kyn Therapeutics, which received $28 million from venture capitalists in 2016! If that wasn’t enough, he is also the co-inventor on 15 patents and patent applications, oh, not to mention that he’s currently working on a drug that would help in battling cancer.
Tying back to his blacksmithing passion, Stone states that the theme of his career has been making tools, some of which are good enough to become medicines. A researcher by day and a blacksmith by night, Stone lives a double life, incorporating creativity with problem solving in both.
On October 10, the Army Research Office (ARO) MURI award headed by Michael Jewett at Northwestern University was held in Austin, Texas, with collaborators Eric Anslyn (Chemistry), Andy Ellington (Molecular Biosciences), Charles Schroeder (University of Illinois Urbana Champaign(UIUC)), Jeff Moore (UIUC), Eric Gaucher (University of Georgia), and Rhiju Das (Stanford University). This diverse team is attempting to recast the ribosome not as a protein-making machine, but as a more generic polymer-making machine. Already, recombinant protein production by the ribosome has transformed the lives of millions of people through the synthesis of biopharmaceuticals, like insulin, and industrial enzymes, like subtilisin, that are used in laundry detergents. In nature, however, only limited sets of protein monomers are utilized, thereby resulting in limited sets of biopolymers (i.e., proteins). Here, the team seeks to expand nature’s repertoire of ribosomal monomers to yield new classes of enzymes, therapeutics, materials, and chemicals with diverse genetically encoded chemistry. To this end, they have developed new technologies for charging tRNAs with non-amino acid substrates using Flexizymes (ribozyme tRNA synthetases) and have engineered other aspects of the translation machinery, including Elongation Factor Tu and the ribosome itself, to be able to utilize these non-standard monomers to make decidedly non-protein polymers. Overall, the goal of the group is to develop a means of making sequence-defined, electronically active polymers for any of a variety of applications of commercial and defense importance.
By Shaharyar Lakhani
Dr. Andy Ellington and his team from the Center for Systems and Synthetic Biology have been awarded a grant from the National Center for Complementary and Integrative Health (NCCIH) to search for and better understand minor compounds produced by cannabis that could potentially aid in the alleviation of pain (https://nccih.nih.gov/news/press/09192019). To this end, Dr. Ellington and his co-workers have developed an extremely novel system for the production and assay of cannabinoids … in yeast! By using yeast as vehicles for screening, rather than plants, it becomes far easier to divide down the heady chemical mixtures that are present in the plant, and better define the particular active agents and what pain receptors these active agents may act on. The use of cannabinoids like CBD as a treatment for chronic pain has become increasingly popular, and might one day even serve as an alternative to opioids, which are highly addictive and aren’t as effective in the long run.
By Shaharyar Lakhani
Earlier this year, Dr. Sanchita Bhadra and her team from the Ellington Lab at UT Austin built a kit that would make research easier to conduct in low resource areas. The kit is intended for students and instructors in these low-resource areas due to its cost effectiveness and ease of use. This would especially prove beneficial in giving research opportunities to aspiring researchers in need of a lab, allowing them to carry out procedures such as PCR using cellular reagents. (https://ellingtonlab.org/archive/2019/7/8/a-solution-to-research-in-low-resource-areas)
Since then, Dr. Bhadra and her team have also been working with scientists at Cambridge University and their research partners in various African countries to assess the utility of cellular reagents in molecular biology research and education. In initial studies, ready-to-use cellular reagents were sent to researchers in Cameroon and Ghana who were able to successfully perform PCR using these reagents. Cellular reagents seamlessly replaced pure enzymes in existing PCR protocols and performed robustly despite the vagaries of shipping and variations in humidity and temperature during storage. These exciting results demonstrating cellular reagents to be reliable alternatives to expensive pure enzymes have paved the way towards efforts in local production and more extensive outreach. Researchers in both UK and Africa are beginning to use expression constructs and production protocols developed in the Ellington Lab to undertake in-house production of cellular reagents. Starting with these foundational efforts, our global team aims to develop, test, and make freely available a comprehensive suite of common enzymatic reagents for molecular and synthetic biology.
By Shaharyar Lakhani
Most plastic items are manufactured from small base substances called nurdles. Nurdles are tiny round pellets of plastic that are saturating coasts around the globe. These pellets carry toxins, and are therefore detrimental to the wildlife that inhabits these environments by getting in their food. Beaches in Port Aransas seem to be saturated with nurdles, and if something isn’t done soon, the biodiversity in areas like this could decrease substantially.
Researchers at the University of Texas at Austin are trying to solve this problem by using a unique approach. In collaboration with the Ellington lab, the Bioprospecting stream of the Freshman Research initiative led by Moriah Sandy ran experiments on microplastics using plastic degrading microbes from plants and monitoring their activity. So far, the team has found bacteria and fungi growing on three types of plastic: polystyrene, polypropylene, and polyethylene. Hannah Cole, a graduate student in both the Ellington and Alper labs is expanding on this research, specifically studying a bacterium that grows on PET plastic, a plastic commonly used in packaging. Cole’s aim is to find a way to mutate the enzymes in the bacteria to degrade the plastic more quickly. While Hannah has seen success in reducing degradation time, there is still the problem of keeping these enzymes efficient at higher temperatures.
These efforts reflect both environmental consciousness and an appreciation of economics. Cole, Sandy, and the bioprospecting team are attempting to not only degrade plastics using microbes, but also to convert their byproducts into something useful. In this way, it may be possible to create a new ‘plastics cycle,’ in which better designed, biodegradable materials go into the environment, and organisms bring the raw materials back out again.