A novel method developed by University of Illinois researchers could change the way metabolic engineering is done.
Researchers from the Carl R. Woese Institute for Genomic Biology’s Biosystems Design theme, including Huimin Zhao, the Steven L. Miller Chair of Chemical and Biomolecular Engineering, recently published a paper in Nature Communications outlining their new method, which could make the metabolic engineering process more efficient.
Metabolic engineering involves engineering microorganisms to produce value-added products such as biofuels and chemicals. This is achieved by changing or deleting the expression of genes to modify the microorganism’s genome. In this process, several targets in the genome are modified in order to achieve specific goals.
“We can easily find several metabolic engineering targets to improve the desired phenotype,” said Jiazhang Lian, a visiting research associate at the IGB who is a co-author of the paper. “How to combine these beneficial genetic modifications is one of the biggest challenges in metabolic engineering.”
Traditionally, researchers test these targets individually in a series of time-consuming steps. These steps limit productivity and the yield of the final product — two crucial components in the metabolic engineering process.
The researchers decided to create a method that combines all of these steps and executes them simultaneously, making the process faster and easier.
They based this method on the CRISPR system, a method of genetic manipulation that uses a set of DNA sequences to modify genes within a cell.
This system uses three genetic manipulations that are frequently used in metabolic engineering: transcriptional activation, transcriptional interference, and gene deletion.
By using these manipulations simultaneously, scientists can explore different combinations of manipulations and discover which combination is best.
“We can now work with 20 targets,” Zhao said. “We can implement all of these (manipulations) for each target in a combinatorial manner to find out which combination actually will give us higher productivity or yield of the final product.”
The researchers tested the method in a species of yeast that is used in winemaking, baking, and the production of biofuels. They showed that using this method could improve the production of a specific product.
Their system, called CRISPR-AID, will allow researchers to easily explore all the possible target combinations. But the key is to find the optimal combination.
“If we compare metabolic engineering to a basketball team, we cannot build a strong team by simply putting the best players together,” Lian said. “Instead, we should try to find those who can collaborate and work synergistically.”
Their new system opens up thousands — even millions — of possibilities, which presents another logistical challenge.
They plan to find the best combinations by developing a high throughput screening method or using a robotic system such as the iBioFAB, a system located in the IGB that automatically produces synthetic biosystems.
“I believe the combination of CRISPR-AID with high throughput screening and iBioFAB will significantly advance the metabolic engineering field in the near future,” Lian said.
Zhao hopes to test their method on other organisms, using the same engineering principles but modifying the protocol for different organisms.
Eventually, they hope to extend to the genome scale — to be able to test all the genes in an organism at once — which would be a considerable leap in the field of metabolic engineering.
“If we can do that, we can make it truly modularized and also standardize the procedure,” Zhao said. “Then we really increase the throughput and the speed of metabolic engineering.”
Several research efforts aim to engineer microorganisms for the production of biofuels and chemicals, so any tools that can speed up the process are significant. Zhao believes this is true for their method.
“It’s not just an incremental improvement,” he said. “It’s a new way to do metabolic engineering.”
Congratulations to Huimin Zhao, who has been chosen to receive the 2018 Marvin Johnson Award from the Biochemical Technology Division of the American Chemical Society!
The Marvin J. Johnson Award in Microbial and Biochemical Technology recognizes outstanding research contributions toward the advancement of microbial and biochemical technology.
Zhao is the Steven L. Miller Chair of Chemical and Biomolecular Engineering, and a professor of chemistry, biochemistry, biophysics, and bioengineering at Illinois. His primary research interests are in the development and applications of synthetic biology tools to address society’s most daunting challenges in health, energy, and sustainability, and in the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation.
The award will be presented to Zhao at the 2018 Spring National Meeting of the ACS on March 18-22, 2018. At that meeting, Zhao will deliver a lecture on his research. Read more about Dr. Huimin Zhao.
Chemical and Biomolecular Engineering faculty member Brendan Harley and a team of researchers from the Carl R. Woese Institute for Genomic Biology’s Regenerative Biology and Tissue Engineering theme were awarded a National Science Foundation grant that will provide funding for a new 3D-bioprinting instrument.
The Major Research Instrumentation grant will fund the purchase of an EnvisionTEC 3D-Bioplotter, a bioprinting system that is essentially a 3D printer for tissues.
Much of the research in the Regenerative Biology and Tissue Engineering (RBTE) theme involves developing approaches to regenerate tissues in order to address problems of human health. But this is not a simple task, considering human tissues are all uniquely complex.
Bioprinting, which uses 3D printing technology to create cell patterns and fabricate biomaterials, will allow researchers to print materials that closely resemble human tissues.
Unlike many 3D printers, which print metals or other hard materials, this bioplotter will let researchers print a wide variety of materials — including materials that are similar in consistency to toothpaste, as well as materials that are the size of human hair or smaller.
“This bioplotter really allows us to do all that,” said Brendan Harley, Associate Professor of Chemical and Biomolecular Engineering and theme leader. “It really lets us open up the toolbox of the materials we can use.”
The bioplotter will be housed within IGB as a shared-use facility that will be accessible to researchers across campus.
Several research efforts at the IGB and the University of Illinois are dedicated to developing tissue engineering solutions that could impact a range of important healthcare issues such as cancer, stem cell behavior and more.
Harley hopes researchers will look to the IGB and the RBTE theme as a hub for tissue engineering on campus.
He said 3D bioplotters have finally become capable of reliably printing at the scale needed to produce complex tissues, and with the acquisition of this printer, IGB will be at the forefront of tissue engineering research.
“We’re going to be able to do some really exciting new work,” he said. “Everything’s in place to really attack big, challenging problems.”
By Emily Scott, IGB Science Writer and Outreach Specialist
The National Science Foundation has awarded a $1.2 million, three-year grant to four professors in Chemical and Biomolecular Engineering for a project that has potential to advance the frontiers of 3-D printing. Drs. Charles Sing, Ying Diao, Damien Guironnet, and Simon Rogers intend to create a platform for designing advanced materials that allows makers to tune the structure and function of a material on-the-fly.
Not long after arriving on campus, the team of investigators, each an assistant professor with a different research background and set of skills, got together to brainstorm what intriguing challenges they could solve together. Take camouflage. Camouflage is only effective as long as the person wearing it remains crouched in the jungle or standing by a sand dune in the desert. What if you had a material that could provide camouflage in many different environments, and you control how it works? Chameleons change color by adjusting skin structure at nanometer-length scales. Could humans design something similar with advanced materials processing?
“What we’re talking about is making a device, an object, instrument, from ostensibly the same material. It has different properties in different parts of the material,” Rogers said. Imagine a Lego brick that has one transparent wall, but the brick is made from all the same material. There’s one material with different properties, and the maker controls the material’s properties.
The project has two overarching goals: develop a screening method for versatile, 3-D printable block copolymer materials, which are two or more different polymer chains linked together; and screen to optimize flow-based tuning of morphology in 3-D printed materials. That entails testing their hypothesis that tuning the flow in 3-D printing will allow for on-the-fly or on-demand manipulation. Insights gained from their research could have potential applications in camouflage, antireflection coatings, metamaterials and displays.
For this project, each faculty member brings a distinct set of skills and expertise. Charles Sing, who works in molecular simulation and theory, will provide what he described as a treasure map. His research will guide the synthesis that occurs in the lab of Damien Guironnet, the self-described “cook.” Because Sing will be predicting some of the molecule’s properties beforehand, Guironnet will be able to synthesize the molecules that will make the polymers with the unique structure needed for the process.
From there, the material is handed over to Simon Rogers and members of his lab, who carefully control different flow conditions and investigate how the structures reorganize. Rogers then feeds information gleaned from his experiments and analysis to Ying Diao’s group. Diao will take the novel molecule and, with the knowledge of how this material reacted to Rogers’ experiments, she will attempt to make a functional material using 3-D printing.
Rogers then feeds information gleaned from his experiments and analysis to Ying Diao’s group. Diao will take the novel molecule and, with the knowledge of how this material reacted to Rogers’ experiments, she will attempt to make a functional material using 3-D printing.
“One key issue we’re interested in is the assembly, how to direct the assembling of the materials because it’s critical to the function,” Diao said. “In this case, we’re interested in the photonic properties. Can we potentially make camouflage using this functional material by assembling the material into highly ordered structures? We’ll be able to sensitively modulate the structure over length scales predicted by Charles Sing.”
What they’re doing could be called a “high-risk, high-reward” type of project, Diao said, because proposing to physically change structure on the fly is a fairly new idea. “The challenge is, how the assembly of this novel class of materials respond to flow is previously unknown. Flow-directed 3D printing is also not demonstrated before and requires significant innovation to realize,” she said.
Faculty anticipate discoveries and some surprises along the way because the material they’ll be working with is new and the process, called non-equilibrium processing, is still a relatively new concept, they said.
The grant comes from the NSF’s Designing Materials to Revolutionize and Engineer our Future (or DMREF) program, which specifically funds projects that aim to develop advanced materials quickly and at a fraction of the cost.
What makes the project unique is each investigator has a role to play in each other’s research. Due to the iterative, multi-project investigator structure, there will be a lot of coordination involved and each faculty member will need to understand results from their colleagues to be able to apply it to their own research.
“It’s an exciting challenge,” Guironnet said. “We get the opportunity to understand each other’s work to increase the impact of our own research. And at the same time, I get to extend my expertise as well,” he said.
What’s also unique about the group is that each investigator is an assistant faculty member. They all joined the department within about a year of each other.
“Because we’re new professors, there’s been a focus on building our own reputations, our own lab expertise. This is our moment to do something bigger than that, and that is extremely exciting,” Sing said.
Thanks to the NSF funding, faculty also plan to expand their outreach projects in computation, characterization and synthesis, via the Girls’ Adventures in Math, Engineering and Science (GAMES) summer camp and the St. Elmo Brady STEM Academy, which exposes underrepresented elementary students to STEM fields.
Congratulations to Dr. Ying Diao, Assistant Professor of Chemical and Biomolecular Engineering, and graduate student Zahra Shamsi. Both were honored by the School of Chemical Sciences for their teaching excellence in the 2016-2017 school year.
“The award recognizes the entire scope of our educational efforts, from course development to in-class instruction. Excellence in teaching is not only intellectually satisfying, but our instructional efforts immeasurably strengthen our research mission,” said Dr. Jonathan Sweedler, director of the School of Chemical Sciences.
Diao, a Dow Chemical Company Faculty Scholar, pursues fundamental understanding and control of molecular assembly processes to advance innovations in printed electronics for energy and healthcare. She joined the department in 2015 and earned her PhD from MIT and her BS from Tsinghua University.
Other faculty recipients of the award for 2016-2017 include So Hirata and Christian Ray from the Department of Chemistry.
Zahra Shamsi is a 3M Fellow and member of Dr. Diwakar Shukla‘s research group. She earned her BS and MS from the Sharif University of Technology in 2014 and joined the department in 2015.
Other graduate students who received the award include Nels Anderson, Emily Geddes, and Yusef Shari’ati from Chemistry.
Congratulations to Ashlee Ford Versypt and Meagan Lewis, both alumni of Chemical and Biomolecular Engineering at Illinois, for being recognized on AIChE’s 35 Under 35 list for 2017.
The winners were announced this week in CEP, Chemical Engineering Progress magazine.
Recipients were chosen for their significant contributions to the American Institute of Chemical Engineers and to the chemical engineering profession. The award was created to acknowledge the successes of some of its youngest members, all under the age of 35, and to promote the achievements of this generation of chemical engineers who are changing the face of the profession, according to AIChE.
Each award winner was selected for their achievements in one of seven categories: bioengineering, chemicals, education, energy, innovation, leadership, and safety. An awards reception will be held at the 2017 AIChE Annual Meeting this fall.
Versypt is Assistant Professor in Chemical Engineering at Oklahoma State University. She directs the Systems Biomedicine and Pharmaceutics Research Laboratory, which focuses on the intersection of chemical engineering, computational science and engineering, applied mathematics, biomedical science, and pharmaceutical science. She received her MS and PhD degrees in Chemical Engineering from Illinois in 2009 and 2012, studying under Prof. Richard Braatz.
Lewis is Senior Product Line Manager at Honeywell UOP and serves on AIChE’s board of directors. She received her BS in Chemical Engineering at Illinois in 2008 and also has an MBA from Loyola University Chicago.
The Department of Chemical and Biomolecular Engineering is pleased to welcome Dr. Svetlana Mitrovski. She joined the department in July as a Teaching Associate Professor.
Dr. Mitrovski joins the department following 10 years as an Associate Professor at Eastern Illinois University in Charleston. At EIU, she taught a variety of chemistry courses to undergraduate and graduate students: instrumental analysis, quantitative analysis, general chemistry courses, critical reading of chemistry literature, and more.
“I’m happy to be back,” said Mitrovski, who earned a PhD in Chemistry from the University of Illinois in 2006, studying PDMS-based microfluidic devices that operate on electrochemical principles under Ralph Nuzzo, the G.L. Clark Professor of Chemistry. She conducted postdoctoral research with Dr. Nuzzo following her graduation.
“One thing that I really liked about Illinois is that chemistry and chemical engineering were coupled in a single school. I liked that because before I came to the USA, I used to work in an area of catalysis that is interdisciplinary between the two,” she said.
A native of Serbia, Mitrovksi earned her BS in Chemical Technology and her MS in Physical Chemistry, Electrochemistry and Electrochemical Engineering from the University of Belgrade. Before coming to the U.S. to further her graduate education, she worked as a researcher at the Center for Catalysis and Chemical Engineering at the Institute of Chemistry, Technology and Metallurgy at the University of Belgrade doing fundamental and industrial research.
Mitrovski will teach “CHBE 430: Unit Operations Lab” and other courses, such as “CHBE 121: The ChBE Profession.”
“I’m looking forward to diving deeper into the undergraduate chemical engineering curriculum and trying to have some impact on it,” she said. “I’m also looking forward to serving as a pipeline or liaison between the undergraduate program and research faculty.”
In her free time, Dr. Mitrovski enjoys ballroom dancing, traveling, hiking, and swimming.
Congratulations to Dr. Huimin Zhao, recipient of the 2017 Award for Excellence in Biological Engineering Publication!
The Biotechnology Progress Award for Excellence in Biological Engineering Publication recognizes outstanding contributions to the literature in biomedical engineering, biological engineering, biotechnology, biochemical engineering and related fields. The award, which is underwritten by John Wiley & Sons, celebrates excellence and foundational contributions to biotechnology and biological engineering through a body of work: a seminal paper, a review, a research report, or other material of significant interest and importance.
The award will be presented a the annual meeting of the American Institute of Chemical Engineers in November.
Zhao is the Steven L. Miller Chair of Chemical and Biomolecular Engineering, and a professor of chemistry, biochemistry, biophysics, and bioengineering at Illinois. His primary research interests are in the development and applications of synthetic biology tools to address society’s most daunting challenges in health, energy, and sustainability, and in the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation. Read more about Dr. Zhao.
Program to form new insight on the brain, expand participation in field of brain science
The National Science Foundation recently granted the University of Illinois $3 million for an interdisciplinary graduate student training program to help form new insight on the brain—and to expand participation in the field of brain science itself.
Sixty graduate students from across campus will participate in the five-year National Science Foundation (NSF) Research Traineeship, led by Martha Gillette, professor of cell and developmental biology and director of the Neuroscience Program. Hyunjoon Kong, professor in chemical and biomolecular engineering, is the lead co-principal investigator.
The project’s primary goal is to provide students with an immersive research experience that blends techniques from multiple disciplines to better understand the many aspects of the human body’s most complex organ.
The program will teach students to use and understand miniature brain machinery critical to examining and regulating brain activities. It’s also designed to increase the participation of women, underrepresented minorities, and students with disabilities in the field of brain science.
A third goal is to improve scientists’ communication skills with the public.
“This is a training initiative between neuroscience and engineering. It’s building on some of the new technologies in engineering, but it’s focused on better understanding the brain,” Gillette said. “It’s exciting because it’s going to let us do new things and train graduate students in new ways.”
Students will come from several departments across campus, including neuroscience, cell and developmental biology, molecular and integrative physiology, chemistry, psychology, chemical and biomolecular engineering, bioengineering, and electrical and computer engineering.
The training program will bridge two research paradigms about the brain: cognitive and behavioral studies, including the use of bioimaging and computational tools to understand adaptation, decision-making, psychology, and learning of an individual; and cell and tissue studies, with a focus on altering cell activity through a variety of methods.
To meet these goals, the program will guide graduate students through specialized courses to broaden their knowledge beyond their own specific fields. Training courses will address behavior and the development of the nervous system as well as engineering, biological, and psychological perspectives on how brain activity can be modified.
The U of I project was one of only three proposals aimed at understanding the brain selected for this particular NSF project, out of a large national competition. Co-directors on the project include Rashid Bashir, professor of bioengineering and electrical and computer engineering and head of the Department of Bioengineering; Neal Cohen, professor of psychology; and Jonathan Sweedler, professor of chemistry.
Students also will have opportunities to visit and work with the laboratories of international partners, including the Institute of Bioengineering and Nanotechnology of A*STAR (Singapore), the Biomedical Research Institute of the Korean Institute of Science and Technology (S. Korea), the University of Tokyo (Japan), the University of Okayama (Japan), the University of Birmingham (U.K.), and the Johannes Gutenberg-University at Mainz (Germany).
While the funding mainly contributes to a training program for graduate students, the project also has a research component. Gillette expects the project to advance a relatively new field of study regarding how, through cross-talking, groups of cells behave differently than the entity that they’re part of.
“The idea of using these self-organizing neuron preparations is new,” Gillette said. “It’s new enough that over the five years of the grant and training period, it will really develop a lot, especially with the technologies we have.”
The U of I’s interdisciplinary approach fits with the NSF’s focus for the training program.
“Integration of research and education through interdisciplinary training will prepare a workforce that undertakes scientific challenges in innovative ways,” said Dean Evasius, director of the NSF Division of Graduate Education. “The NSF Research Traineeship awards will ensure that today’s graduate students are prepared to pursue cutting-edge research and solve the complex problems of tomorrow.”
By Samantha Jones Toal, College of Liberal Arts and Sciences
The Department of Chemical and Biomolecular Engineering will celebrate the legacy of the late Illinois Chemical Engineering Professor Thomas J. Hanratty this fall during Homecoming weekend.
The weekend will include presentations and discussions on the long-lasting impact of Dr. Hanratty’s teaching and research, opportunities to reconnect with fellow students and colleagues, and the chance to learn about fluid mechanics research at Illinois today.
Speakers will include Professor Ron Adrian, Professor Jonathan Higdon, Dr. John Kuzan, Professor Mark McCready, Professor Dimitrios Papavassiliou, and more.
Please visit the event page to learn more about the itinerary and how to register.
Highlights of the weekend
Friday, Oct. 27, 2017
Informal welcome lunch.
Afternoon: Technical presentations.
Evening: cocktails, appetizers and reflections.
Saturday, Oct. 28
9 a.m. Alumni tailgate outside Memorial Stadium.
Option to attend the Homecoming football game. Illinois will face Wisconsin at 11 a.m.
Evening drinks and dinner with fellow Hanratty students and colleagues at the Illini Union.